Jagannath Mondal wrote:
HI,
I am a gromacs beginner. I am trying to simulate a non natural peptide. I have prepared a standalone molecule .itp file for my molecule and I have prepared a corresponding topology file(topol.top) which include the .itp file.

First, I was trying to get a .gro file from the PDB file of my molecule. But, when-ever I try to use the pdb2gmx command it always ask to choose among the shared topologies present in gromacs library in stead of refering to my own topology file present in working directory. And it also over-writes my own topology file. My question is : 1. How can I prepare a .gro file using my own topogy file from my PDB file i.e How I can force the gromacs to look into my present directory in stead of looking into the shared gromacs topologies ?

if you have .top you don't need to run pdb2gmx
you can use pdb file as input to grompp

2. I have one more query. What is the use of 'define' string in toplgy files?
chapter 5 in the manual

   Thanks.
 Jagannath MOndal
_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
[EMAIL PROTECTED]       [EMAIL PROTECTED]   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to