[gmx-users] Re:pdb files and force field

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 9 12:12:15 CEST 2009

Bhawana Gupta wrote:
> hello sir,
> Thankyou for the reply.
> The pdb file i had taken from the TINKER is the one where force field 
> used is oplsaa.
> when i use this file in gromacs.it <http://gromacs.it> give error of 
> atom type.

It is always better to post the exact error message.  What tool are you using 
that complains?

> when i had gone in top folder which is in gromacs where all the force 
> fields are defined.
> its written that you must define it yourself.

Define what?

> i don't know how to do that.
> My peptide is Ace-Arg-Pro-Val-Thr-NMe
> its giving error in the atom type of NMe(N-methyl)
> i had changed its name from NMe to NAC as defined in the forcefield.
> But another error came for Ace i.e. its CH3 atomtype not found.

If you are using pdb2gmx, you must ensure that all of the constituent residues 
have all the necessary atoms and they are named exactly how the force field 
expects them to be named.  You will have to fix whatever inconsistencies there 
are between your .pdb file and what the force field expects.


> Tell me want to do.
> Should i send you my pdb file???
> So that u can help me better.
> with regards
> Bhawana
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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