I am very grateful for all these advices...
On Fri, Jul 5, 2013 at 9:02 PM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> > 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 Sun Jul 07 2013 - 11:30:02 PDT
