Sanku M wrote:
Hi,
I have a protein pdb file with ACE as N-cap and I am trying to use
pdb2gmx ( within gromacs 4.5.4 ) to generate a topology file using
opls/AA . the ACE is present in opls aminoacids.rtp files. But, on
issuing the pdb2gmx command, I get following error message:
Program pdb2gmx_44, VERSION 4.5.4
Source code file: pdb2top.c, line: 1070
Fatal error:
atom N not found in buiding block 1ACE while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
I wonder how I can make sure that ACE can be used as N-terminus.
You've somehow constructed the cap wrong. There is no N atom in ACE. Check the
.rtp for what's required, check your coordinate file, and make sure you're using
"-ter none" with pdb2gmx. If that's still not working, post your command and
relevant snippet of your coordinate file.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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