Hi,
Try cpptraj from AmberTools 17, or better yet the GitHub version. I vaguely
remember fixing something related to extra points a while back so maybe
that's the issue you are encountering.
-Dan
On Tue, Jul 18, 2017 at 5:57 PM Ming Tang <m21.tang.qut.edu.au> wrote:
> 16
>
> Sent from my Huawei Mobile
>
> Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> What version of cpptraj are you using?
>
> -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
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>
>
>
> --
> -------------------------
> 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
>
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--
-------------------------
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
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Received on Wed Jul 19 2017 - 03:30:02 PDT
