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

Erik Marklund erikm at xray.bmc.uu.se
Tue Jun 19 09:51:43 CEST 2007

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?

> 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
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys

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