[gmx-users] Hi..

Navratna Vajpai navratna.vajpai at unibas.ch
Wed Aug 16 11:49:40 CEST 2006

Many thanks Eric, it worked. I didn't really had look into this.
Best regards

On Aug 16, 2006, at 11:34 AM, Erik Marklund wrote:

> On Wed, 2006-08-16 at 10:07 +0200, David van der Spoel wrote:
>> Navratna Vajpai wrote:
>>> Hey Mark..
>>> I had attached the file along with the mail. I think you could
>>> not receive it. let me paste the contents and explain it little  
>>> more.
>>> I am trying to run the simulation in vacuum of a nona peptide. I  
>>> managed
>>> to get pdb2gmx working and even further the EM working. But when  
>>> I tried
>>> to do the MD run after a small minimization of protein, I got an  
>>> error
>>> message after the execution of grompp. The execution asked for  
>>> the -n
>>> option which indicates for the index file. 1) I don't know why it  
>>> asked for?
> My guess it's because of this line in the mdp file:
> tc-grps     =  protein      sol
> Apparently you have temperature-coupled the solvent, even though you
> have no solvent. Vacuum, right? Note that grompp is looking for 'sol'
> and, when it can't find it among the default groups (see manual), it
> looks for an index file:
> Fatal error:
> Group sol not found in indexfile.
> Maybe you have non-default goups in your mdp file, while not using the
> '-n' option of grompp.
> In that case use the '-n' option.
> Try removing 'sol' from the mdp file. If you are simulating in vacuum,
> you (probably) have no solvent.
> /Erik
>>> 2) If it ask for is there any way to solv this problem. Actually  
>>> i tried
>>> using that also. But the error stayed back.
>>> I am also pasting the error after the grompp. Somehow this could not
>>> prepare the input file for the MD run.
>>> 3) third question is: I am wondering whether i can start my run just
>>> after the execution of pdb2gmx. Any ways 1) the system is in  
>>> vacuum and
>>> second while running it for quite long, minimization of energy will
>>> automatically take place.
>> You should probably start by doing the tutorial and browsing the web
>> site, check out the flow chart for doing simulations.
> -- 
> Erik Marklund, PhD Student, Molecular Biopcysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone: +46 18 471 4537          fax: +46 18 511 755
> erikm at xray.bmc.uu.se
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Navratna Vajpai
Ph. D student in Prof. Grzesiek's laboratory
Department of Structural Biology
Biozentrum, University of Basel
Klingelbergstrasse 70,
Basel, Switzerland.
Phone- +41 61 267 2080(O)
	       +41 78 744 0810(M)

navratna.vajpai at unibas.ch

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