AMBER: problems in energy minimization using TIP5P water model

From: sugino tatsuro <>
Date: Mon, 15 Jan 2007 01:35:11 +0900

Dear AMBER users,

As for my question on TIP5P model in AMBER, I would like to add some
information of my status.

Before perturbation, I performed energy minimization by using the system
composed of 1293 TIP5P water molecules created by xLeap. But their
coordinates were not changed in the calculation, and little of the total
energy of the system was decreased.

Still, after that I carried out standard MD calculation, and it was
performed without problems.

Here, I retrieved topology and coordinate files of the system using the
following commands;

> loadamberparams gaff.dat
> source TIP5P.cmd
> loadamberparams parm99EP.dat
> loadamberparams frcmod.tip5p
> model = TP5
> solvatebox model TP5 20
> saveamberparm model parm.crd

In addition, I attached an xleap.log file generated by xLeaP program and
an mdout file generated through minimization.

Thank you very much in advance for any help.

Best wishes,

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Received on Wed Jan 17 2007 - 06:07:15 PST
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