[gmx-users] multiple pdb of same protein complex

Javier Cerezo jcb1 at um.es
Wed Jan 16 12:14:05 CET 2013

You could use a script to do all runs consecutively using one pdb file 
at a time. Anyway, if what you have are different conformations of the 
same system, the same topology should apply for all of them, so just 
need to obtain it once.


El 16/01/13 12:07, Serdar Durdagi, PhD escribió:
> I would like to analyze the different conformations (~1000 structures) 
> of a protein/protein complex using GROMACS. Can I list all of these 
> pdb files within a text file when I start the pdb2gmx; i.e., text file 
> that includes:
> 0001.pdb
> 0002.pdb
> ....
> or is there any other ways to handle this problem?
> many thanks,
> Serdar

Ph.D. Student
Physical Chemistry
Universidad de Murcia
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