[gmx-users] DNA simulation

David spoel at xray.bmc.uu.se
Thu Nov 28 19:55:51 CET 2002

On Thu, 2002-11-28 at 20:45, Luke Czapla wrote:
> Hi All,
>   I am able to use the residues DADE for A and DTHY for T (etc), but some
> of the hydrogens need to be added (some of the side chain ones on the
> bases) and I was wondering if this can be done by modifying the hdb file.
>   I am going to try to check the source code for pdb2gmx and try to make a
> suitable workaround.  As far as uracil parameterization, John, I am
> working in Wilma Olson's lab and we are quite enthusiastic about
> parameterization of such things.  Maybe we could keep in touch, since I am
> at Rutgers and in the same town and campus.  I know AMBER/CHARMM are
> generally more suitable but there have been very good results with the
> GROMOS87 force field and having open source code for GROMACS is very
> promising since there is a lot of new ideas we have for force field
> development which may be implementable and I'm considering my own GPL
> fork of the source code if MD is the direction of my thesis research (DNA
> -protein interactions is the big picture).
Although you are ofcourse entitled to make your own fork of the code
according to the GPL, I think it would be beneficial if you contribute
your edits directly to the gromacs source (since we are also entitled to
take your edits and put it back into gromacs under the GPL). Something
like DNA/protein interactions is definitely in the interest of many

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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