On 5/23/12 1:26 PM, ankita oindrila wrote:
i am stimulting an AMP protein in water.
this is the error i get on my first step..
pdb2gmx -f 1PG1_1.pdb -o 1PG1_1_processed.gro -water spce
error:
Fatal error: atom C not found in buiding block 19NH2 while combining
tdb and rtp
please HELP!!
I suspect you're not selecting your termini correctly. If NH2 is a capping
residue, you need to interactively select termini (using the -ter option) and
specify them as "None." Otherwise, pdb2gmx treats all residues as normal amino
acids and tries to build normal amino and carboxylate termini.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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