> I am facing an error when I use amber99 forcefield in Gromacs. I am not
> aware on what may be the cause of the following error on a single strand
> thymine. When I remove the P (phosphate) atom everything work without
> problem. Since DNA contains P, I would like to know if anyone my advise me
You are much more likely to get useful help from the Gromacs e-mail list
as most AMBER users reading this list use AMBER...
Note that the AMBER force fields typically do not include a 5'-terminal
phosphate so check if that is the issue. Also, your error seems to be on
recognizing a water residue (HOH).
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b
Note also that this force field is dated for nucleic acids; minimally you
likely need to include the parmbsc0 modifications of Perez et al.
otherwise you will get a tendency of gamma->trans.
> Thank you for any suggestion
Finally, I loaded up that PDB file into Chimera and the base structure
appears highly distorted and there appear to be multiple atoms with the
same name (H3?) and the names do not correspond to standard DNA naming
conventions so there could be issues with the nucleic acid structure.
For more help, seek out the Gromacs list.
--tec3
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Received on Fri Jul 05 2013 - 14:30:02 PDT
