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
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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 Thu Jul 20 2017 - 06:30:04 PDT
