quick and dirty fix: you could use the gromacs trjconv command with a
suitable index group (!aMW) to output everything except the tip4p MW atoms
in the gromacs trajectory to fake a tip3p system, which I presume can be
analyzed properly with cpptraj. Not sure what your full usage is, but if
needed you can also create a new gromacs .tpr file based on a new, modified
topology that uses tip3p and a .pdb/.gro file that you have similarly
stripped the MW pseudo-atoms from.
Obviously if there is an issue then one wants to eventually fix it in
Amber, but this might be enough to get you going for now.
On Tue, Jul 18, 2017 at 3:56 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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> > 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
>
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Received on Tue Jul 18 2017 - 21:30:03 PDT
