Avogadro建出来的核酸末端都是多一个磷酸基团的，删掉即可。

Shuang-Jie 发表于 2023-5-17 17:11
Atom OXT in residue U 1 was not found in rtp entry RU with 28 atoms

GROMACS:      gmx pdb2gmx,  ...

楼主您好，我也是遇到同样的问题，有的RNA里的基团，比如PSU,OMG,OMU,2MA,5MC,这些特殊的A,U,G,C非常奇怪，在itp中不能找到，如果强制替换成A,U,G,C，后面的模拟也会报错，有的基团在进行能量最小化后会跑出RNA，这个应该怎么办呀？

喵星大佬 发表于 2023-5-18 02:02
Amber力场的核酸参数没有端基磷酸化的定义，改用charmm

Atom OXT in residue U 1 was not found in rtp entry RU with 28 atoms

GROMACS:      gmx pdb2gmx, version 2020.6-MODIFIED
Executable:   C:\gmx2020.6_GPU\bin\\gmx.exe
Data prefix:  C:\gmx2020.6_GPU
Working dir:  D:\shuangjie
Command line:
  gmx pdb2gmx -ignh -f 1.pdb -o 1.gro -p 1.top -ter


Select the Force Field:
From 'C:/gmx2020.6_GPU/share/gromacs/top':
1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
2: AMBER14SB_parmbsc1
3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
9

Using the Charmm27 force field in directory charmm27.ff

Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/watermodels.dat

Select the Water Model:
1: TIP3P   TIP 3-point, recommended
2: TIP4P   TIP 4-point
3: TIPS3P  CHARMM TIP 3-point with LJ on H's
4: TIP5P   TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
5: SPC     simple point charge
6: SPC/E   extended simple point charge
7: None
1
going to rename charmm27.ff/aminoacids.r2b
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/aminoacids.r2b
going to rename charmm27.ff/rna.r2b
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/rna.r2b
Reading 1.pdb...
WARNING: all CONECT records are ignored
Read 'UNNAMED', 473 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 22 residues with 473 atoms

  chain  #res #atoms
  1 'A'    22    473

All occupancies are one
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/atomtypes.atp
Reading residue database... (Charmm27)
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/aminoacids.rtp
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/dna.rtp
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/lipids.rtp
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/rna.rtp
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/dna.hdb
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/rna.hdb
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/dna.n.tdb
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/rna.n.tdb
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/dna.c.tdb
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/rna.c.tdb
Processing chain 1 'A' (473 atoms, 22 residues)
Identified residue U1 as a starting terminus.
Identified residue G22 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for U-1
0: NH3+
1: NH2
2: 5'
3: None
2
Start terminus U-1: 5'
Select end terminus type for G-22
0: COO-
1: COOH
2: CT2
3: CT3
4: 3'
5: None
4
End terminus G-22: 3'
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/aminoacids.arn
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/dna.arn
Opening force field file C:\gmx2020.6_GPU/share/gromacs/top/charmm27.ff/rna.arn

-------------------------------------------------------
Program:     gmx pdb2gmx, version 2020.6-MODIFIED
Source file: src\gromacs\gmxpreprocess\pdb2gmx.cpp (line 745)

Fatal error:
Atom OXT in residue U 1 was not found in rtp entry RU with 28 atoms
while sorting atoms.
.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Shuang-Jie 发表于 2023-5-17 17:39
老师这个问题我明白了，请问端基的磷酸基团这么处理呢？

Amber力场的核酸参数没有端基磷酸化的定义，改用charmm

sobereva 发表于 2023-5-13 15:46
参考北京科音分子动力学与GROMACS培训班ppt

老师这个问题我明白了，请问端基的磷酸基团这么处理呢？

喵星大佬 发表于 2023-5-12 19:47
-ter

我使用了-ter也还是同样报错”Atom OXT in residue U 1 was not found in rtp entry RU5 with 28 atoms“

喵星大佬 发表于 2023-5-12 19:47
-ter

是这么用嘛“gmx pdb2gmx -ignh -ter -f 151.pdb -o 151.gro -p topol.top”，求指导

sobereva 发表于 2023-5-13 15:46
参考北京科音分子动力学与GROMACS培训班ppt

嗯嗯，谢谢老师解答。那我怎么解决这个“Residue 'RU5' not found in residue topology database”呢？

Shuang-Jie 发表于 2023-5-13 11:40
关键是我的.pdb文件里面，没有RU5这个残基呀

参考北京科音分子动力学与GROMACS培训班ppt

Shuang-Jie 发表于 2023-5-12 22:35
Residue 'RU5' not found in residue topology database

关键是我的.pdb文件里面，没有RU5这个残基呀

喵星大佬 发表于 2023-5-12 19:47
-ter

Residue 'RU5' not found in residue topology database

-ter