[gmx-users] topology file for DNA molecule

tenghl hailong at seas.ucla.edu
Thu Sep 30 06:42:25 CEST 2004

Hello Andrey,

Thank you for you reply. Is there any method that I can use GROMACS to simulate DNA molecule?
I have read several papers which talk about the simulation of DNA, and the software they used is GROMACS.



*********** REPLY SEPARATOR  ***********

On 9/30/2004 at 10:15 AM Andrey V. Golovin wrote:

>Hello Discussion,
>9/30/2004, 8:15 AM you wrote:
>tenghl> Dear Gromacs users,?
tenghl> ?
tenghl> I am trying to build a
>topology file for a DNA model
>tenghl> using pdb2gmx -f file.pdb -p file.top -o file.gro.
>tenghl> I used OPLS force field and got the following error, any
tenghl> Sorting it all out...
>tenghl> Opening library file /space/gromacs/share/top/ffoplsaa.hdb
>tenghl> Opening library file /space/gromacs/share/top/ffoplsaa-n.tdb
>tenghl> Opening library file /space/gromacs/share/top/ffoplsaa-c.tdb
>tenghl> Processing chain 1 (438 atoms, 20 residues)
>tenghl> Opening library file /space/gromacs/share/top/specbond.dat
>tenghl> 5 out of 5 lines of specbond.dat converted succesfully
>tenghl> There are 0 donors and 0 acceptors
>tenghl> There are 0 hydrogen bonds
>tenghl> Fatal error: Residue 'A5' not found in residue topology database
>This happened because OPLSA ff in gromacs doesn't contain any DNA/RNA
>residues in rtp file. We added it and now busy with checking. Checking
>is necessary because we added some dihedrals. I hope soon this files
>can be found in contribution section.
>tenghl> ?
tenghl> Thanks
>tenghl> ?
tenghl> Hailong
>Best regards,
>Andrey                          mailto:golovin at genebee.msu.su
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