[gmx-users] DNA simulations with GROMACS???

Anna Reymer anna.reymer at gmail.com
Tue Jun 19 09:31:26 CEST 2007

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.


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