Hi Dan,
We found a quick and dirty fix around this problem. We converted gro file
to pdb. Pdb will wrap the residue numbering. Ming is interested in
nativecontact calculation with solvent. From pdb we used the writeparm
option to get prmtop file. We also used solvent command to define tip4p.
Prmtop doesn't include exact force field parameters but it is ok as we are
only interested in figuring out neighbouring residues through out the
trajectory.
Cheers,
Neha
On 20 Jul 2017 23:24, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> Also, if you would like you can send me off-list a trajectory and
> topology file that illustrates the problem and I can try to check
> things out for you.
>
> -Dan
>
> On Mon, Jul 17, 2017 at 10:08 PM, Ming Tang <m21.tang.qut.edu.au> wrote:
> > Dear list,
> >
> > I did a simulation in GROMACS using oplsaa with TIP4P water, and want to
> investigate the residues within 0.3 nm of a cation throughout the
> trajectory using 'nativecontacts' in CPPTRAJ. I found amber cannot
> recognise TIP4P water from GROMACS. If I do the native contact analysis for
> the trajectory without water, it give me correct results. However, If I do
> it for the trajectory with water, it does not print any contacts, not even
> the contact between the cation and protein. Besides, I found that distance
> between the cation and its nearby atoms in the protein is not correct, but
> the distance between atoms in the protein is correct. The pbc effects in
> the trajectory was already eliminated in gromacs. Also, I tried to use
> autoimage in amber with the protein fixed and non-protein free. But it did
> not work. Then, I tried to change the atom types of the solvent in my
> trajectory to match those of TIP4P water in AMBER, and it did not work
> either.
> >
> > Could anybody help to give me some suggestion?
> > Any help is appreciated,
> > Ming
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 21 2017 - 03:00:03 PDT
