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标题: GROMACS里短链RNA建模和拓扑文件生成方法 [打印本页]

作者
Author: Shuang-Jie 时间: 2023-5-12 19:05
标题: GROMACS里短链RNA建模和拓扑文件生成方法
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。
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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。

作者
Author: 喵星大佬 时间: 2023-5-12 19:47
-ter

作者
Author: Shuang-Jie 时间: 2023-5-12 22:35
本帖最后由 Shuang-Jie 于 2023-5-13 11:30 编辑

喵星大佬发表于 2023-5-12 19:47
-ter

Residue 'RU5' not found in residue topology database

作者
Author: Shuang-Jie 时间: 2023-5-13 11:40

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

作者
Author: sobereva 时间: 2023-5-13 15:46

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

(, 下载次数 Times of downloads: 45)

作者
Author: Shuang-Jie 时间: 2023-5-13 20:14

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？

作者
Author: Shuang-Jie 时间: 2023-5-17 16:24

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

作者
Author: Shuang-Jie 时间: 2023-5-17 17:38

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“

作者
Author: Shuang-Jie 时间: 2023-5-17 17:39

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？

作者
Author: 喵星大佬 时间: 2023-5-18 02:02

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

作者
Author: Shuang-Jie 时间: 2023-5-18 08:58
本帖最后由 Shuang-Jie 于 2023-5-18 18:02 编辑

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？
(, 下载次数 Times of downloads: 42)

作者
Author: Shuang-Jie 时间: 2023-5-18 09:11

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

作者
Author: 欢乐多 时间: 2024-5-6 01:00
本帖最后由欢乐多于 2024-5-5 13:54 编辑

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？

作者
Author: mol 时间: 2024-8-4 16:43
Avogadro建出来的核酸末端都是多一个磷酸基团的，删掉即可。

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