[gmx-users] topology file for DNA molecule

Andrey V. Golovin golovin at genebee.msu.su
Thu Sep 30 08:45:07 CEST 2004

Hello tenghl,

9/30/2004, 8:42 AM you wrote:

first of all could you send me links for papers =) as i know gromacs
was used only for trajectory analysis.
And certainly you can use G43a1 ff. But first you should rename A to
DADE, C to DCYT, G to DGUA, T to DTHY.

tenghl> Hello Andrey,

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

tenghl> Thanks,

tenghl> Hailong

tenghl> *********** REPLY SEPARATOR  ***********

tenghl> 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
>>gmx-users mailing list
>>gmx-users at gromacs.org
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tenghl> _______________________________________________
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Best regards,
Andrey                          mailto:golovin at genebee.msu.su

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