[gmx-users] Coarse-Grain: GROMACS bond information to VMD
Nicolas Sapay
nicolas.sapay at cermav.cnrs.fr
Wed Oct 21 17:52:34 CEST 2009
Hello everybody,
Here is the rtf file I mentioned previously. It can be used by PSFGEN to
generate a psf file from pdb files. The result can be used, for example,
by the PME Electrostatics plugin of VMD. PSFGEN is available as a VMD
plugin or as an independant executable.
Nicolas
Nicolas SAPAY a écrit :
> Hi,
>
> All TCL scripts dowloaded from the VMD website as well as mine are
> supposed to be used within VMD. You have to run VMD first, then source the
> script. Alternatively, you can source it in your .vmdrc file. After that,
> you can run the g_cg function
>
> Nicolas
>
>
>> <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
>> <html>
>> <head>
>> <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
>> <title></title>
>> </head>
>> <body bgcolor="#ffffff" text="#000000">
>> HI all,<br>
>> <br>
>> 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.<br>
>> <br>
>> Another question: <br>
>> How to use the code from Nicolas? I got the following error information
>> from <br>
>> >>>> ./coarse_grain.tcl -tpr em.tpr<br>
>> <br>
>> : command not found line 10:<br>
>> ./coarse_grain.tcl: line 14: proc: command not found<br>
>> : command not found line 15:<br>
>> ./coarse_grain.tcl: line 17: global: command not found<br>
>> ./coarse_grain.tcl: line 18: global: command not found<br>
>> ./coarse_grain.tcl: line 19: global: command not found<br>
>> ./coarse_grain.tcl: line 20: global: command not found<br>
>> ./coarse_grain.tcl: line 21: global: command not found<br>
>> ./coarse_grain.tcl: line 22: global: command not found<br>
>> ./coarse_grain.tcl: line 23: global: command not found<br>
>> ./coarse_grain.tcl: line 24: global: command not found<br>
>> ./coarse_grain.tcl: line 25: global: command not found<br>
>> : command not found line 26:<br>
>> : command not found line 41:<br>
>> : command not found line 45:<br>
>> ./coarse_grain.tcl: line 120: syntax error near unexpected token `}'<br>
>> '/coarse_grain.tcl: line 120: ` } else {<br>
>> <br>
>> best wishes,<br>
>> Baofu Qiao<br>
>> <br>
>> Nicolas SAPAY wrote:
>> <blockquote
>> cite="mid:49e9485f32667c27440f5b0b836a3bf4.squirrel at webmail.cermav.cnrs.fr"
>> type="cite">
>> <blockquote type="cite">
>> <pre wrap="">Justin A. Lemkul wrote:
>> </pre>
>> <blockquote type="cite">
>> <pre wrap="">I have also added a Perl script to the GROMACS site
>> (the VMD page):
>>
>> <a class="moz-txt-link-freetext"
>> href="http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD">http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD</a>
>>
>> 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.
>> </pre>
>> </blockquote>
>> <pre wrap="">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.
>> </pre>
>> </blockquote>
>> <pre wrap=""><!---->
>> 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
>>
>> </pre>
>> <blockquote type="cite">
>> <pre wrap="">Mark
>>
>> </pre>
>> <blockquote type="cite">
>> <pre wrap="">Nicolas Sapay wrote:
>> </pre>
>> <blockquote type="cite">
>> <pre wrap="">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 :
>> </pre>
>> <blockquote type="cite">
>> <pre wrap="">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
>>
>>
>> </pre>
>> </blockquote>
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>> <pre wrap=""><!---->
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