[gmx-users] CHARMM FF and cmap

[Justin A. Lemkul]

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
> 
> 

-- 
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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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