19 jun 2007 kl. 09.31 skrev Anna Reymer:
Dear GROMACS users!
Is it possible to model DNA with the help of GROMACS with AMBER ports?
I've checked mailing-list and found that the only GROMCAS force field
appropriate for modeling DNA is OPLS, but it does not provide good
enough results for long DNA MD runs.
The mailing-list suggested AMBER ports. I've managed to produce
topology and coordinates files, solvate the system. But when I came to
grompp step, I got the following error message:
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448
Fatal error:
number of coordinates in coordinate file (genbox.gro, 32804)
does not match topology (dick.top, 0)
---
I've checked my dick.top file and it looks OK. I've also checked
ffamber99.rtp, ffamber99.atp, ffamber.hdb,ffamberbon.itp and several
other files. I am not a programmer myself, but I checked the same sort
of files for GROMOS force fields, they have different format and I
suspect that this is the reason for the error message. The program
simply can't parse some files.
Has someone tried modelling DNA in GROMACS with AMBER ports? Was it
successful?
Thank you all in advance.
I have, and it works just fine. I suspect there is indeed something
wrong with your top-file. Check your #includes. What does your
[ molecules ] section look like?
/Erik
regards,
Anna
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
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