GROMACS里短链RNA建模和拓扑文件生成方法

Shuang-Jie

各位老师好，想模拟Micro RNA151【5’ -UAACACUGUCUGGUAAAGAUGG- 3’】在水盒子中的结构，在老师的建议下，采用Avogadro-build-Insert-DNA/RNA输入对应的碱基序列，简单优化后，另存为151.pdb;
贴结构如下，.pdb完整文档参照附件。




按老师建议：
输入
【gmx pdb2gmx -ignh -f 151.pdb -o 151.gro -p topol.top】，力场选择【 2: AMBER14SB_parmbsc1】，水模型选择【 1: TIP3P     TIP 3-point, recommended】
报错:
Fatal error:
Atom OXT in residue U 1 was not found in rtp entry RU5 with 28 atoms
while sorting atoms.
查看了相应力场文件目录中【rna.rtp】里面的RU5，确实没有OXT的定义。
[ RU5 ]
[ atoms ]
   H5T    HO            0.42950     1
   O5'    OH           -0.62230     2
   C5'    CI            0.05580     3
  H5'1    H1            0.06790     4
  H5'2    H1            0.06790     5
   C4'    CT            0.10650     6
   H4'    H1            0.11740     7
   O4'    OS           -0.35480     8
   C1'    CT            0.06740     9
   H1'    H2            0.18240    10
    N1    N*            0.04180    11
    C6    C2           -0.11260    12
    H6    H4            0.21880    13
    C5    C2           -0.36350    14
    H5    HA            0.18110    15
    C4    C             0.59520    16
    O4    O            -0.57610    17
    N3    NA           -0.35490    18
    H3    H             0.31540    19
    C2    C             0.46870    20
    O2    O            -0.54770    21
   C3'    CT            0.20220    22
   H3'    H1            0.06150    23
   C2'    CT            0.06700    24
  H2'1    H1            0.09720    25
   O2'    OH           -0.61390    26
  HO'2    HO            0.41860    27
   O3'    OS           -0.52460    28
麻烦问老师，我怎么操作才能把模拟继续进行下去呢？我看论有帖子说OXT是终止的元素，可以直接删除，是确定可以删除么？如果替换，参照什么标准替换呢？
而且同时，151.pdb里面的'P'原子，[ RU5 ]也没有定义。就是我怎么在pdb2gmx步骤中去处理磷酸基团呢？求老师指导！

附件是151.pdb和AMBER14SB_parmbsc1目录中的rna.rtp文件。

喵星大佬

-ter

Shuang-Jie

喵星大佬 发表于 2023-5-12 19:47
-ter

Residue 'RU5' not found in residue topology database

Shuang-Jie

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

sobereva

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

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

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

Shuang-Jie

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“

Shuang-Jie

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

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

Shuang-Jie

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

老师，貌似charmm27.ff也没有定义末端的P-OH,这个羟基该怎么处理呢？

Shuang-Jie

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
-------------------------------------------------------

欢乐多

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？

mol

Avogadro建出来的核酸末端都是多一个磷酸基团的，删掉即可。