Hi Song,
Your suggestion is indeed correct. The ACEMD misses out the bond
information for TIPS3P.
Cheers, Neha
On 22 July 2016 at 22:57, Song-Ho Chong <chong.sookmyung.ac.kr> wrote:
> Hi,
>
> Check RESI TIP3 part of top file downloaded from ACEMD.
> If the BOND part is
>
> BOND OH2 H1 OH2 H2
>
> you should add H1 and H2 at the end, so that
>
> BOND OH2 H1 OH2 H2 H1 H2
>
> Also, you need to be extremely careful in handling par file
> downloaded from ACEMD (C22STAR part).
> It contains more than one dihedral term of the same
> multiplicity (n), which may not be appropriately handled
> by the tools you are using.
> If you are not sure, you can modify them by yourself
> by referring to posts in charmm forum.
>
> SHC
>
> 2016-07-22 20:58 GMT+09:00 Neha Gandhi <n.gandhiau.gmail.com>:
>
> > Dear List,
> >
> > I downloaded top and par files for charmm22* force field available at
> ACEMD
> > website. I then used VMD to create psf and pdb files using psfgen,
> solvate
> > and ionize plugins of vmd. It seems vmd writes out psf in xplor format.
> >
> > I then used chamber with nocmap option to convert psf and pdb files to
> > prmtop and inpcrd. However, I get this error.
> >
> > Error: A residue defined as a "fast 3-point water"
> > is not defined by a triangle of three bonds.
> > Residue 24 contains 2 bonds.
> >
> > The amber files generated by charmm-gui runs without error.
> >
> > Does chamber support xplor psf format?
> >
> >
> >
> >
> >
> > --
> > Regards,
> > Dr. Neha S. Gandhi,
> > Vice Chancellor's Research Fellow,
> > Queensland University of Technology,
> > 2 George Street, Brisbane, QLD 4000
> > Australia
> > LinkedIn
> > Research Gate
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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Received on Fri Jul 22 2016 - 06:30:02 PDT
