VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Aug 31 2014 - 10:38:00 CDT

On Sun, Aug 31, 2014 at 5:33 PM, sunyeping <sunyeping_at_aliyun.com> wrote:
>
> I have no idea about a _complete_topology file without any includes and
> preprocessor directives. Could you give me an example?

read the gromacs docs or ask the gromacs folks. this is a gromacs
issue. top2psf.pl expects a .top file without any of those. this
question has come up multiple times in the past.

>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
>
> ------------------------------------------------------------------
> 发件人：Axel Kohlmeyer <akohlmey_at_gmail.com>
> 发送时间：2014年8月31日(星期日) 23:28
> 收件人：孙业平 <sunyeping_at_aliyun.com>
> 主　题：Re: 答复：vmd-l: c_top2psf.pl
>
> please always reply to the mailing list. i already explained what your
> problem is. please re-read my e-mail.
>
> On Sun, Aug 31, 2014 at 5:27 PM, sunyeping <sunyeping_at_aliyun.com> wrote:
>>
>> ------------------------------------------------------------------
>> 发件人：Axel Kohlmeyer <akohlmey_at_gmail.com>
>> 发送时间：2014年8月31日(星期日) 00:21
>> 收件人：孙业平 <sunyeping_at_aliyun.com>
>> 抄　送：vmd-l <vmd-l_at_ks.uiuc.edu>
>> 主　题：Re: vmd-l: c_top2psf.pl
>>
>> On Sat, Aug 30, 2014 at 5:14 PM, sunyeping <sunyeping_at_aliyun.com> wrote:
>>> Dear all,
>>>
>>> In VMD script library there is a script c_top2psf.pl. This is to
>>> transform
>>> top file into psf file.
>>>
>>> I used this command line to do the transformation:
>>>
>>> perl c_top2psf.pl -p topol.gro -o topol.psf
>>>
>>> However, the only content of the psf it generated is:
>>>
>>> PSF
>>> 4 !NTITLE
>>> REMARKS TOPOLOGY CREATED BY PERL SCRIPT (MARC BAADEN)
>>> REMARKS contact baaden smplinux.de
>>>
>>> 0 !NATOM
>>>
>>> 0 !NBOND: bonds
>>>
>>> Maybe I misused this script. Could you tell me how I can get a normal psf
>>> file which contains the atom cooridnations?
>>
>> a) you use a .gro file and not a topology file. you need a _complete_
>> topology file without any includes and preprocessor directives.
>> b) a .psf file contains no coordinates.
>>
>>
>>
>>
>>
>> That's a type mistake. In fact I use topol.top as the input file. The
>> content of the topol.top is:
>>
>> ;
>> ; File 'topol.top' was generated
>> ; By user: root (0)
>> ; On host: localhost.localdomain
>> ; At date: Wed Nov 13 23:18:27 2013
>> ;
>> ; This is a standalone topology file
>> ;
>> ; It was generated using program:
>> ; pdb2gmx - VERSION 5.0-dev
>> ;
>> ; Command line was:
>> ; pdb2gmx -f KI-10_ABC_intact.pdb -ignh -o complex.gro
>> ;
>> ; Force field was read from the standard Gromacs share directory.
>> ;
>>
>> ; Include forcefield parameters
>> #include "gromos53a6.ff/forcefield.itp"
>>
>> ; Include chain topologies
>> #include "topol_Protein_chain_A.itp"
>> #include "topol_Protein_chain_B.itp"
>> #include "topol_Protein_chain_C.itp"
>>
>> ; Include water topology
>> #include "gromos53a6.ff/spc.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ; i funct fcx fcy fcz
>> 1 1 1000 1000 1000
>> #endif
>>
>> ; Include topology for ions
>> #include "gromos53a6.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> Protein in water
>>
>> [ molecules ]
>> ; Compound #mols
>> Protein_chain_A 1
>> Protein_chain_B 1
>> Protein_chain_C 1
>>
>> SOL 18007
>> NA 62
>> CL 55
>>
>>
>> Is this a complete topology file?
>> Then I use c_top2psf.pl:
>>
>> perl c_top2psf.pl -p topol.top -o topol.psf
>>
>> The content of the output psf file is:
>>
>> PSF
>> 4 !NTITLE
>> REMARKS TOPOLOGY CREATED BY PERL SCRIPT (MARC BAADEN)
>> REMARKS contact baaden smplinux.de
>>
>> 0 !NATOM
>>
>> 0 !NBOND: bonds
>> What is the error about my input or usage of this script? Thanks.
>>
>>
>>
>>
>>>
>>> Best regards.
>>>
>>>
>>>
>>>
>>> Yeping
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.