amber构建蛋白配体复合物参数时报错

流卡瓦

我在用amber20构建蛋白质小分子复合物时，小分子生成参数时tleap没有错误，当我将小分子的pdb内容复制到蛋白质的pdb构建com.pdb后，执行com.tleap,文件如下
source leaprc.protein.ff19SB
source leaprc.water.tip3p
source leaprc.gaff
loadamberparams Y.frcmod
loadoff Y.lib
complex = loadpdb com.pdb
check complex
solvatebox complex TIP3PBOX 12.0
addions2 complex Na+ 0
addions2 complex Cl- 0
saveamberparm complex X_box.prmtop X_box.inpcrd
savepdb complex X_box.pdb
quit

出现如下报错
Bond: Maximum coordination exceeded on .R<QY7 292>.A<H 5>
      -- setting atoms pert=true overrides default limits
ATOMS NOT BONDED: .R<QY7 292>.A<C 2> .R<QY7 292>.A<H 5>
!FATAL ERROR----------------------------------------
!FATAL:    In file [/home/yaohua/Downloads/amber20_src/AmberTools/src/leap/src/leap/atom.c], line 441
!FATAL:    Message: bondAtomProblem found
!
!ABORTING.
这个小分子可以在gromacs里正常进行模拟
请问是我小分子参数化的有问题吗，我要如何在amber中构建蛋白配体复合物。

sylar

1. HETATM    1  N   QY7A   1      40.078 -37.864 -63.462  0.00  0.00
   
2. HETATM    2  N   QY7A   1      39.166 -40.555 -65.749  0.00  0.00
   
3. HETATM    3  N   QY7A   1      36.504 -42.103 -66.708  0.00  0.00
   
4. HETATM    4  N   QY7A   1      34.845 -41.413 -65.205  0.00  0.00
   
5. HETATM    5  N   QY7A   1      34.458 -40.985 -63.874  0.00  0.00

复制代码

小分子原子名不能重复，你的PDB里面所有同类原子名都是元素类型，手动改成如下试试

1. HETATM    1  N1  QY7A   1      40.078 -37.864 -63.462  0.00  0.00
   
2. HETATM    2  N2  QY7A   1      39.166 -40.555 -65.749  0.00  0.00
   
3. HETATM    3  N3  QY7A   1      36.504 -42.103 -66.708  0.00  0.00
   
4. HETATM    4  N4  QY7A   1      34.845 -41.413 -65.205  0.00  0.00
   
5. HETATM    5  N5  QY7A   1      34.458 -40.985 -63.874  0.00  0.00

复制代码

sylar

流卡瓦 发表于 2022-8-25 10:55
我在修改完之后再次执行，输出了如下报错
FATAL:  Atom .R.A does not have a type.
FATAL:  Atom .R.A ...

改最开始的那个PDB，改完整个流程重走一遍。

hangmint

sylar 发表于 2022-8-25 13:54
改最开始的那个PDB，改完整个流程重走一遍。

话说这个小分子力场做了没？

sylar

hangmint 发表于 2022-8-25 21:36
话说这个小分子力场做了没？

做了，但他改原子名后还是用之前的frcmod和lib，所以不匹配

流卡瓦

谢谢指导，问题是出在这个原子名上面了，我重新生成了个原子名不同的pdb文件，可以正常参数化了，
我还有个小问题，在我运行pmemd.cuda完成时会有一个如下的note
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
这个正常吗？

valiente1

流卡瓦 发表于 2022-8-26 15:03
谢谢指导，问题是出在这个原子名上面了，我重新生成了个原子名不同的pdb文件，可以正常参数化了，
我还有 ...

楼主，我现在也出现了这个问题，运行pmemd.cuda完成时会有：The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL，请问你了解是什么原因了嘛

MYSY08

sylar 发表于 2022-8-26 09:07
做了，但他改原子名后还是用之前的frcmod和lib，所以不匹配

您好，我遇到了类似的问题。我在用amber构建DNA小分子复合物时，当我载入力场载入DNA后检查DNA参数时发生了报错
base) shisheng@shisheng-System-Product-Name:~/MD/FB1/27 5C-A bc$ tleap -f leap2.in
-I: Adding /home/shisheng/software_wtao/amber20/dat/leap/prep to search path.
-I: Adding /home/shisheng/software_wtao/amber20/dat/leap/lib to search path.
-I: Adding /home/shisheng/software_wtao/amber20/dat/leap/parm to search path.
-I: Adding /home/shisheng/software_wtao/amber20/dat/leap/cmd to search path.
-f: Source leap2.in.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./leap2.in
----- Source: /home/shisheng/software_wtao/amber20/dat/leap/cmd/leaprc.DNA.bsc1
----- Source of /home/shisheng/software_wtao/amber20/dat/leap/cmd/leaprc.DNA.bsc1 done
Log file: ./leap.log
Loading parameters: /home/shisheng/software_wtao/amber20/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading library: /home/shisheng/software_wtao/amber20/dat/leap/lib/parmBSC1.lib
Loading parameters: /home/shisheng/software_wtao/amber20/dat/leap/parm/frcmod.parmbsc1
Reading force field modification type file (frcmod)
Reading title:
Parmbsc1 force-field for DNA
Loading PDB file: ./dna_removeH.pdb
Created a new atom named: P within residue: .R<DA5 1>
Created a new atom named: OP1 within residue: .R<DA5 1>
Created a new atom named: OP2 within residue: .R<DA5 1>
Created a new atom named: OP3 within residue: .R<DA5 1>
  total atoms in file: 550
  Leap added 309 missing atoms according to residue templates:
       309 H / lone pairs
  The file contained 4 atoms not in residue templates
Checking 'dna'....

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
The unperturbed charge of the unit (-26.000000) is not zero.
FATAL:  Atom .R<DA5 1>.A<P 31> does not have a type.
FATAL:  Atom .R<DA5 1>.A<OP1 32> does not have a type.
FATAL:  Atom .R<DA5 1>.A<OP2 33> does not have a type.
FATAL:  Atom .R<DA5 1>.A<OP3 34> does not have a type.

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.120313 angstroms between .R<DA5 1>.A<H8 13> and .R<DA5 1>.A<OP1 32>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 0.973280 angstroms between .R<DA5 1>.A<N9 11> and .R<DA5 1>.A<OP3 34>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.012149 angstroms between .R<DA5 1>.A<C1' 9> and .R<DA5 1>.A<OP3 34>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.382856 angstroms between .R<DA5 1>.A<O4' 8> and .R<DA5 1>.A<OP3 34>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.499471 angstroms between .R<DA5 1>.A<P 31> and .R<DA5 1>.A<OP2 33>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.141055 angstroms between .R<DC 14>.A<O2 24> and .R<DT 17>.A<H73 20>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 0.993172 angstroms between .R<DT 26>.A<H71 18> and .R<DT3 27>.A<H72 19>
Checking parameters for unit 'dna'.
Checking for bond parameters.
Checking for angle parameters.
check:  Errors:  4   Warnings: 8
----- Source: /home/shisheng/software_wtao/amber20/dat/leap/cmd/leaprc.gaff
----- Source of /home/shisheng/software_wtao/amber20/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/shisheng/software_wtao/amber20/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
Loading parameters: ./lig.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Loading Mol2 file: ./lig.mol2
Reading MOLECULE named UNK
Checking 'lig'....
Checking parameters for unit 'lig'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
Checking 'com'....

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
The unperturbed charge of the unit (-25.998001) is not zero.
FATAL:  Atom .R<DA5 1>.A<OP3 34> does not have a type.
FATAL:  Atom .R<DA5 1>.A<OP2 33> does not have a type.
FATAL:  Atom .R<DA5 1>.A<OP1 32> does not have a type.
FATAL:  Atom .R<DA5 1>.A<P 31> does not have a type.

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 0.993172 angstroms between .R<DT3 27>.A<H72 19> and .R<DT 26>.A<H71 18>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.324736 angstroms between .R<DT 21>.A<H72 19> and .R<UNK 28>.A<H52 102>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.141055 angstroms between .R<DT 17>.A<H73 20> and .R<DC 14>.A<O2 24>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 0.615652 angstroms between .R<DA 6>.A<H61 20> and .R<UNK 28>.A<H25 75>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.437049 angstroms between .R<DA 6>.A<H61 20> and .R<UNK 28>.A<C10 26>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.382856 angstroms between .R<DA5 1>.A<OP3 34> and .R<DA5 1>.A<O4' 8>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.012149 angstroms between .R<DA5 1>.A<OP3 34> and .R<DA5 1>.A<C1' 9>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 0.973280 angstroms between .R<DA5 1>.A<OP3 34> and .R<DA5 1>.A<N9 11>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.499471 angstroms between .R<DA5 1>.A<OP2 33> and .R<DA5 1>.A<P 31>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.120313 angstroms between .R<DA5 1>.A<OP1 32> and .R<DA5 1>.A<H8 13>
Checking parameters for unit 'com'.
Checking for bond parameters.
Checking for angle parameters.
check:  Errors:  4   Warnings: 11
----- Source: /home/shisheng/software_wtao/amber20/dat/leap/cmd/leaprc.water.tip3p
----- Source of /home/shisheng/software_wtao/amber20/dat/leap/cmd/leaprc.water.tip3p done
Loading library: /home/shisheng/software_wtao/amber20/dat/leap/lib/atomic_ions.lib
Loading library: /home/shisheng/software_wtao/amber20/dat/leap/lib/solvents.lib
Loading parameters: /home/shisheng/software_wtao/amber20/dat/leap/parm/frcmod.tip3p
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP3P water
Loading parameters: /home/shisheng/software_wtao/amber20/dat/leap/parm/frcmod.ions1lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set)
Loading parameters: /home/shisheng/software_wtao/amber20/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
Loading parameters: /home/shisheng/software_wtao/amber20/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)
(using default radius 1.500000 for OP3)
(using default radius 1.500000 for OP2)
(using default radius 1.500000 for OP1)
(using default radius 1.500000 for P)
  Solute vdw bounding box:              40.430 30.679 42.991
  Total bounding box for atom centers:  60.430 50.679 62.991
  Solvent unit box:                     18.774 18.774 18.774
(using default radius 1.500000 for OP3)
(using default radius 1.500000 for OP2)
(using default radius 1.500000 for OP1)
(using default radius 1.500000 for P)
  Total vdw box size:                   63.312 53.470 65.734 angstroms.
  Volume: 222529.237 A^3
  Mass > 105675.807 amu,  Density > 0.789 g/cc
      (type - hence mass - of one or more atoms could not be found)
  Added 5371 residues.
Total unperturbed charge: -25.998001
Total perturbed charge:   -25.998001
26 K+ ions required to neutralize.
Adding 26 counter ions to "com" using 1A grid
Used default radius  1.50 for 4 atoms
Grid extends from solute vdw + 1.71  to  7.80
Resolution:      1.00 Angstrom.
Calculating grid charges
Placed K+ in com at (3.17, 4.74, 0.75).
Placed K+ in com at (-6.83, 5.74, -2.25).
Placed K+ in com at (6.17, -3.26, -5.25).
Placed K+ in com at (-4.83, -1.26, 8.75).
Placed K+ in com at (-4.83, 6.74, 16.75).
Placed K+ in com at (8.17, 2.74, -31.25).
Placed K+ in com at (-0.83, -13.26, -9.25).
Placed K+ in com at (8.17, 21.74, -31.25).
Placed K+ in com at (-31.83, -3.26, -7.25).
Placed K+ in com at (32.17, 11.74, -5.25).
Placed K+ in com at (2.17, -27.26, 1.75).
Placed K+ in com at (19.17, -14.26, 32.75).
Placed K+ in com at (-29.83, 23.74, -30.25).
Placed K+ in com at (1.17, 4.74, 32.75).
Placed K+ in com at (32.17, -4.26, -14.25).
Placed K+ in com at (-16.83, -27.26, 1.75).
Placed K+ in com at (0.17, 25.74, 13.75).
Placed K+ in com at (-10.83, 22.74, -31.25).
Placed K+ in com at (-17.83, -14.26, 32.75).
Placed K+ in com at (12.17, 27.74, -17.25).
Placed K+ in com at (-31.83, -21.26, -8.25).
Placed K+ in com at (1.17, 24.74, 30.75).
Placed K+ in com at (3.17, -26.26, 21.75).
Placed K+ in com at (-31.83, 15.74, -7.25).
Placed K+ in com at (32.17, -4.26, 4.75).
Placed K+ in com at (-31.83, -2.26, -28.25).

Done adding ions.
Checking 'com'....
FATAL:  Atom .R<DA5 1>.A<OP3 34> does not have a type.
FATAL:  Atom .R<DA5 1>.A<OP2 33> does not have a type.
FATAL:  Atom .R<DA5 1>.A<OP1 32> does not have a type.
FATAL:  Atom .R<DA5 1>.A<P 31> does not have a type.

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 0.993172 angstroms between .R<DT3 27>.A<H72 19> and .R<DT 26>.A<H71 18>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.324736 angstroms between .R<DT 21>.A<H72 19> and .R<UNK 28>.A<H52 102>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.141055 angstroms between .R<DT 17>.A<H73 20> and .R<DC 14>.A<O2 24>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 0.615652 angstroms between .R<DA 6>.A<H61 20> and .R<UNK 28>.A<H25 75>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.437049 angstroms between .R<DA 6>.A<H61 20> and .R<UNK 28>.A<C10 26>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.382856 angstroms between .R<DA5 1>.A<OP3 34> and .R<DA5 1>.A<O4' 8>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.012149 angstroms between .R<DA5 1>.A<OP3 34> and .R<DA5 1>.A<C1' 9>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 0.973280 angstroms between .R<DA5 1>.A<OP3 34> and .R<DA5 1>.A<N9 11>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.499471 angstroms between .R<DA5 1>.A<OP2 33> and .R<DA5 1>.A<P 31>

/home/shisheng/software_wtao/amber20/bin/teLeap: Warning!
Close contact of 1.120313 angstroms between .R<DA5 1>.A<OP1 32> and .R<DA5 1>.A<H8 13>
Checking parameters for unit 'com'.
Checking for bond parameters.
Checking for angle parameters.
check:  Errors:  4   Warnings: 10
Checking Unit.
FATAL:  Atom .R<DA5 1>.A<OP3 34> does not have a type.
FATAL:  Atom .R<DA5 1>.A<OP2 33> does not have a type.
FATAL:  Atom .R<DA5 1>.A<OP1 32> does not have a type.
FATAL:  Atom .R<DA5 1>.A<P 31> does not have a type.

/home/shisheng/software_wtao/amber20/bin/teLeap: Fatal Error!
Failed to generate parameters

Exiting LEaP: Errors = 1; Warnings = 29; Notes = 0.

(base) shisheng@shisheng-System-Product-Name:~/MD/FB1/27 5C-A bc$
teap文件为二、（适配体）准备：
reduce -Trim dna.pdb > dna_removeH.pdb  ；去除dna中的氢原子
三、复合物准备：
tleap -f leap2.in ；运行.in文件
source leaprc.DNA.bsc1 ；
dna = loadpdb dna_removeH.pdb ；
check dna ；
source leaprc.gaff ；
loadamberparams lig.frcmod ；
lig = loadmol2 lig.mol2 ；
check lig   ；
com = combine {dna lig} ；
check com ；
source leaprc.water.tip3p ；
solvatebox com TIP3PBOX 10.0 ；
charge com  ；
addIons2 com K+ 0 ；
check com  ；
saveamberparm com com.prmtop com.inpcrd ；
savepdb com com.pdb ；
quit ；

一个一个的输的话是在check dna开始报错
我的DNA链只是一个碱基进行了突变，其他同样流程的DNA都没有出现这种问题。我按照上面的做法改了小分子的文件，但还是报错。我想是我的DNA文件有问题，请您帮忙看看，谢谢。