[gmx-users] pdb2gmx problem

[Justin A. Lemkul]

Warren Gallin wrote:
> Hi,
> 
>     I am trying to set up a simulations of short peptides in water, and 
> I want to eliminate the electrostatic interactions of the N-terminal 
> amino group and the C-terminal carboxyl group by capping them, with 
> acetate for the N-terminus and a C-terminal amide.
> 
>     I built the PDB file using TINKER (see attached file) but when I run:
> 
>     pdb2gmx -f Gly10_Capped.pdb -water tip3p -ignh
> 

You need to specify -ter and choose "None" to add a capping group.

> N-terminus: NH3+
> C-terminus: COO-

Here's your hint: pdb2gmx is assigning default (charged) termini, which is not 
what you want.

> Now there are 12 residues with 79 atoms
> 
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0

I would recommend upgrading to the latest version (4.0.5) to take advantage of 
bug fixes, especially those pertinent to DD stability.

-Justin

> Source code file: pdb2top.c, line: 574
> 
> Fatal error:
> atom N not found in residue 1ACE while combining tdb and rtp
> -------------------------------------------------------
> 
>     The ACE residue does not have a N atom, either in the pdb file or in 
> ffoplsaa.hdb or in ffoplsaa.rtp, so I don't understand what the problem is.
> 
>     Can someone shed some light on this?
> 
> 
> Warren Gallin
> 
> 
> 
>     
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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