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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