[gmx-users] Coarse-Grain: GROMACS bond information to VMD

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 21 14:33:31 CEST 2009 


Baofu Qiao wrote:
> HI all,
> 
> I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD 
> website. But both of them can only deal with single chain system. Take 
> an example, if there are 10 proteins (+water) in my system,  how to 
> convert to topology of the total system to .psf file? I tried to append 
> the .psf. But VMD doesn't recognize the appended .psf file.
> 

I can't comment on Nicolas' script, but as for my own, you need to supply a 
single topology, there is no way to append the output.  You could, for 
visualization purposes, separate the coordinates of each of your subunits from 
the assembled structure, generate the corresponding .psf file for each, and load 
them all separately into VMD.  A little tedious, I know, but given the method 
for generating MARTINI topologies, I'm not sure I can provide a better method.

-Justin

> Another question:
> How to use the code from Nicolas? I got the following error information 
> from
>  >>>> ./coarse_grain.tcl -tpr em.tpr
> 
> : command not found line 10:
> ./coarse_grain.tcl: line 14: proc: command not found
> : command not found line 15:
> ./coarse_grain.tcl: line 17: global: command not found
> ./coarse_grain.tcl: line 18: global: command not found
> ./coarse_grain.tcl: line 19: global: command not found
> ./coarse_grain.tcl: line 20: global: command not found
> ./coarse_grain.tcl: line 21: global: command not found
> ./coarse_grain.tcl: line 22: global: command not found
> ./coarse_grain.tcl: line 23: global: command not found
> ./coarse_grain.tcl: line 24: global: command not found
> ./coarse_grain.tcl: line 25: global: command not found
> : command not found line 26:
> : command not found line 41:
> : command not found line 45:
> ./coarse_grain.tcl: line 120: syntax error near unexpected token `}'
> '/coarse_grain.tcl: line 120: ` } else {
> 
> best wishes,
> Baofu Qiao
> 
> Nicolas SAPAY wrote:
>>> Justin A. Lemkul wrote:
>>>     
>>>> I have also added a Perl script to the GROMACS site (the VMD page):
>>>>
>>>> http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD
>>>>
>>>> The user provides an input topology file, and a .psf file is written,
>>>> which can be loaded as data for the structure in VMD.  The !NBOND
>>>> section seems to be the most important in this regard, so the other
>>>> sections are a bit rough, but it seems to work alright.
>>>>
>>>> The caveat is the topology must be one generated by MARTINI, in order to
>>>> satisfy all the pattern matching and the order of the topology.  It
>>>> should be fairly easy to modify the program further to accommodate other
>>>> layouts, but I haven't had the need to do so.
>>>>       
>>> I added text to the above page describing both scripts, which are
>>> attached. I'd have done that yesterday but the website was
>>> intermittently down.
>>>     
>>
>> Thanks for posting the tcl script on the website, although this script has
>> been mainly coded by someone else. I have simply modified it for my own
>> purpose.
>>
>> I also want to mention it is a good think to create a psf file if one work
>> with VMD. You store at once, bonds, atom types and charges. Actually, I
>> should have somewhere a .rtf file for the Martini amino acids and lipids
>> (the equivalent of the Gromacs rtp file for CHARMM). It can be used by
>> psfgen to generate a psf file with Martini bonds, charges and atom types.
>> If I can retrieve it in my archives, I will post it on the website.
>>
>> Nicolas
>>
>>   
>>> Mark
>>>
>>>     
>>>> Nicolas Sapay wrote:
>>>>       
>>>>> Hello Thomas,
>>>>>
>>>>> I have a tcl script in my personal script library that might do what
>>>>> you want to do. I didn't use it for quite a while, but it was working
>>>>> well as far as I remember. I think it has been adapted from a script
>>>>> available on the VMD website, but I don't remember exactly its
>>>>> history. It doesn't seem too difficult to understand. You should be
>>>>> able to modify it for your own purpose, if needed.
>>>>>
>>>>> Cheers,
>>>>> Nicolas
>>>>>
>>>>>
>>>>> Thomas Schmidt a écrit :
>>>>>         
>>>>>> Dear Omer,
>>>>>>
>>>>>> many thanks for your answer, but your solution doesn't work for me.
>>>>>> We have Protein-Lipid models in the CG scale.
>>>>>> Only if I replace all atom names in the PDB file through "CA" I can
>>>>>> use
>>>>>> the "trace" drawing method, but get also wrong atoms connected to each
>>>>>> other. For example CG Beads with low distances to each other, e.g. in
>>>>>> coarse-grained benzene rings, were not connected. I guess that this
>>>>>> method is distance dependent, too, but in another way. :-)
>>>>>>
>>>>>> Does anybody else have a solution (...to put GROMACS bond information
>>>>>> into VMD)?
>>>>>>
>>>>>> Thomas
>>>>>>
>>>>>>
>>>>>>           
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>>>     
>>
>>
>>   
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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