|
|
本帖最后由 牧生 于 2020-8-12 22:37 编辑
最近在做表面活性剂自组装，花了好大力气才装好了带cuda的gromacs。。目前刚开始做，就遇到了难题。
用MS建立并另存了CTAB+，Br-和水分子的pdb文件，然后用packmol粗略的建立了一个模型（先不管是否很合理），命名为ctab+h2o.pdb
tolerance 2.0
add_box_sides 1.2
output ctab+h2o.pdb
structure water.pdb
number 1000
inside cube 0. 0. 0. 50.
end structure
structure ctab+.pdb
number 50
inside cube 0. 0. 0. 50.
end structure
structure br-.pdb
number 50
inside cube 0. 0. 0. 50.
end structure
end structure
自我感觉似乎也没错
下一步操作：读取pdb文件，生成gro和top文件，使用水模型为tip3p
gmx pdb2gmx -f ctab+h2o.pdb -o ctab+h2o.gro -p ctab+h2o.top -water tip3p
选择力场15 OPLS-AA以后，就报错
Using the Oplsaa force field in directory oplsaa.ff
going to rename oplsaa.ff/aminoacids.r2b
Opening force field file C:\gmx2019.3/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading ctab+h2o.pdb...
Read 'Built with Packmol', 6150 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 3 chains and 0 blocks of water and 1100 residues with 6150 atoms
chain #res #atoms
1 'A' 1000 3000
2 'B' 50 3100
3 'C' 50 50
WARNING: there were 3000 atoms with zero occupancy and 0 atoms with
occupancy unequal to one (out of 6150 atoms). Check your pdb file. #pdb肯定是有问题的，但是作为新人小白，又不太看得出来哪里有问题，或者如何解决
Opening force field file C:\gmx2019.3/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 814
Reading residue database... (Oplsaa)
Opening force field file C:\gmx2019.3/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 51
Sorting it all out...
Opening force field file C:\gmx2019.3/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file C:\gmx2019.3/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file C:\gmx2019.3/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
Back Off! I just backed up ctab+h2o.top to ./#ctab+h2o.top.1#
Processing chain 1 'A' (3000 atoms, 1000 residues)
Warning: No residues in chain starting at 1 identified as Protein/RNA/DNA.
This makes it impossible to link them into a molecule, which could either be
correct or a catastrophic error. Please check your structure, and add all
necessary residue names to residuetypes.dat if this was not correct.
Warning: No residues in chain starting at 2 identified as Protein/RNA/DNA.
This makes it impossible to link them into a molecule, which could either be
correct or a catastrophic error. Please check your structure, and add all
necessary residue names to residuetypes.dat if this was not correct.
Warning: No residues in chain starting at 3 identified as Protein/RNA/DNA.
This makes it impossible to link them into a molecule, which could either be
correct or a catastrophic error. Please check your structure, and add all
necessary residue names to residuetypes.dat if this was not correct.
Warning: No residues in chain starting at 4 identified as Protein/RNA/DNA.
This makes it impossible to link them into a molecule, which could either be
correct or a catastrophic error. Please check your structure, and add all
necessary residue names to residuetypes.dat if this was not correct.
Warning: No residues in chain starting at 5 identified as Protein/RNA/DNA.
This makes it impossible to link them into a molecule, which could either be
correct or a catastrophic error. Please check your structure, and add all
necessary residue names to residuetypes.dat if this was not correct.
Disabling further warnings about unidentified residues at start of chain.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
-------------------------------------------------------
Program: gmx pdb2gmx, version 2019.3
Source file: src\gromacs\gmxpreprocess\resall.cpp (line 618)
Fatal error:
Residue '' not found in residue topology database #我如何解决这个问题啊？
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors #看了手册的说明，这是一个新手常犯的错误，需要残基，但是手册上说的解决办法比较官方，没有实例的解释说明，我理解起来还是比较吃力。
-------------------------------------------------------
得到一个空的top文件
;
; File 'ctab+h2o.top' was generated
; By user: Administrator (-1)
; On host: PCOS-2020NOAPHI
; At date: Wed Aug 12 22:12:38 2020
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2019.3 (-:
;
; Executable: C:\gmx2019.3\bin\gmx.exe
; Data prefix: C:\gmx2019.3
; Working dir: E:\
; Command line:
; gmx pdb2gmx -f ctab+h2o.pdb -o ctab+h2o.gro -p ctab+h2o.top -water tip3p
; Force field was read from the standard GROMACS share directory.
;
; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"
于是怀疑带电的部分是否有问题，重新建立了只有水的pdb，但是运行gmx pdb2gmx还是一样的报错。
附件为我使用的三个文件
br-.pdb
(185 Bytes, 下载次数 Times of downloads: 3)
ctab+.pdb
(6.57 KB, 下载次数 Times of downloads: 6)
water.pdb
(349 Bytes, 下载次数 Times of downloads: 11)
请诸位智者帮帮忙。
|
|
发表于 Post on 2020-8-12 22:24:42
|
只看该作者 Only view this author
|只看大图 View big picture
|倒序浏览 Reverse view
|阅读模式 Reading model
收藏 Add to favorites
发表于 Post on 2020-8-13 07:47:09
楼主 Author
