[gmx-users] rtp file

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 29 15:17:26 CET 2007

Quoting özge kül <ozgekul8233 at yahoo.com>:

> Hi all,
>   I  try to use gromacs for my callculations of thrombin structure.I obtained
> the pdb from protein databank.But the structure has some missing residues at
> the end of the chain and et the beginning of the chain.I completed the
> residues with sybyl 7.3.And then I started to my simulation.But in the
> pdb2gmx command I got this
>   fatal error.:Atom LPD1 in MET11 not found in rtp entry with 9 atoms.

That means the residue has atoms that are named differently than those in the
.rtp file.  If the atom does indeed belong, determine what it is and rename it
in the .pdb file, not the .rtp.

>   Then I looked at the .rtp file.I want to learn how can I add a missing
> thing to the .rtp file.I search for the list that have the same titile.But
> one of you please write me how can I do this.My simulation is depend on this
> fatal error.

You should not make changes to the .rtp file unless you absolutely know what
you're doing.


>   Thank you very much
>   Özge Kül
>   Hacettepe University
>   Chemistry Department
> ---------------------------------
> Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it
> now.


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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