Zuzana Benkova wrote:
Dear GROMACS users,
I would like to run some simulations of systems combined of polyethylene
oxide brushes and short homooligopeptides (alanine, 12 residues) using
CHARMM force field with GROAMCS 4.0.5 version. I have used parameters
from the CHARMM force field files from the newest version of GROMACS. I
have prepared rtp files, converted the dihedral potential from type 9 to
type 3 (Ryckaert-Bellemans) in ffbonded.itp. I can not prepare topol.top
file when using pdb2gms -ff ... -f ... I am geting the following error
message
Program pdb2gmx, VERSION 4.0.3
Source code file: resall.c, line: 344
Fatal error:
in .rtp file in residue cmap at line:
-C N CA C +N
Can I run these simulations with including CMAP.itp in 4.0.5 version. I
have tried to omit the cmap.itp in the forcefield.itp, and removed
[cmap] section in rtp and thus to neglect the CMAP correction, but I
still got the same message. I have checked the mailing list but have not
found answer to my questions. I would be very thanful for any
suggestions and advice
The best idea is to simply use the newest version of Gromacs (4.5.2), since it
has full support for CHARMM, including CMAP. The error you ran into above was
due to a bug that was fixed somewhere in the course of 4.5.x development. There
have been several other pertinent bug fixes, so I think that would be enough
motivation to save yourself a lot of pain and use a version that is actually
advertised as supporting CHARMM :)
-Justin
Greetings
Zuzana
--
========================================
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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