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

[Anna Reymer]

Hi again!

The end of my top file looks :
[ molecules ]
; Compound        #mols
Protein             1
SOL             10682


/Anna

On 6/19/07, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
>
> 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
> erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
>
>
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