rama david wrote:
Hi Gromacs friends,
When I given the command ...
pdb2gmx -f .. -o .. -p .. -ignh
I gate the following error..
------------------------------------------------------
Program pdb2gmx, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/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
When I goes through the detail of the website at
http://www.gromacs.org/Documentation/Errors and document
I come to know that I have to modify the rtp file,
Nowhere in the explanation of the error does it suggest that you should alter
the .rtp file in this instance. You have atoms in your structure that are not
in the .rtp entry. Specifically, your structure file has an N atom in ACE, but
ACE only contains CA, C, and O. The N atom should be the first atom in the next
residue, not ACE.
-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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
