[gmx-users] about porse.itp

[Justin A. Lemkul]

Bhawana Gupta wrote:
> Dear gmx-users,
> 
> i made earlier asked this question .but there is a problem.
>  first i got the error:
> -------------------------------------------------------
> Program grompp, VERSION 4.0
> Source code file: futil.c, line: 527
> 
> Fatal error:
> Library file posre.itp not found in current dir nor in default directories.
> (You can set the directories to search with the GMXLIB path variable)
> 
> Then on your advice, i put posre.itp in my directory, but i again got an 
> error.
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.0
> Source code file: toppush.c, line: 1196
> 
> Fatal error:
> [ file posre.itp, line 9 ]:
> Atom index (5) in position_restraints out of bounds (1-3).
> This probably means that you have inserted topology section 
> "position_restraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "position_restraints" section to the right molecule.
> -------------------------------------------------------

Interestingly, this exact question was asked just a few days ago:

http://www.gromacs.org/pipermail/gmx-users/2008-November/037675.html

It would serve you well to search the archives; many answers can be found there. 
  And furthermore, grompp is giving you advice about how to solve the problem. 
Something in your .top is out of order.

<snip>

> 
> then i again make a posre.itp file , which i like this
> ; In this topology include file, you will find position restraint
> ; entries for all the heavy atoms in your original pdb file.
> 
> [ position_restraints ]
> ; atom  type      fx      fy      fz
> 
> AFTER THAT I GOT NO ERROR.
> TELL ME WHETHER I AM CORRECT AT THIS POINT.
> 

Well, then you're applying no position restraints, which I suppose is not what 
you are after.

-Justin

> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================