Hi, Alan <br>Thank you very much for your quick answer.<br>You understand well my problem...<br>I normally use amb2gmx for proteins, and, changing some residue names (ex. CYM-->CYS..), it works correctly...<br>It's the first time that I work with DNA, and I have this problem... <br>
thank you for your help<br>Rubben<br> <br><div class="gmail_quote">2009/7/1 Alan <span dir="ltr"><<a href="mailto:alanwilter@gmail.com" target="_blank">alanwilter@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi there,<br>
<br>
Not really clear what you did or want to do, so I'll do assumptions.<br>
<br>
If your have you prmtop and inpcrd files working fine with AMBER (sand<br>
or pmemd) then you just want to run this with GMX (mdrun ...).<br>
<br>
So, you can try amb2gmx.pl program or (better), look at<br>
<a href="http://acpypi.googlecode.com" target="_blank">acpypi.googlecode.com</a>, and you can find how to use 'acpypi' for<br>
converting amber topology files to gromacs topol files.<br>
<br>
Cheers,<br>
Alan<br>
<div><div></div><div><br>
On Wed, Jul 1, 2009 at 10:25, <<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>> wrote:<br>
><br>
> Hi, gmx-users, I have a problem to "translate" nitrogen base residue names<br>
> from AMBER to GROMACS.<br>
> I have simulated with AMBER a DNA-protein complex, then i have changed in<br>
> the prmtop file the standard nitrogen bases as DT--> DTHY, DG-->DGUA,<br>
> DC-->DCYT, DA-->DADE, in order to "translate" the MDs from AMBER to<br>
> GROMACS... but in the prmtop file are present also DT5, CT3, that indicate<br>
> the residues at the end of the chains... anyone knows which is the correct<br>
> GROMACS residue name for these residues? I have searched in the ff.rtp file<br>
> but seem that these particular residues are not present...<br>
> Thank you in advance...<br>
<br>
<br>
</div></div>--<br>
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>
Department of Biochemistry, University of Cambridge.<br>
80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a href="http://www.bio.cam.ac.uk/%7Eawd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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