Re: AMBER: MD simulation on a protein solvated by a combination of some water mod

From: David A. Case <>
Date: Thu, 14 Jul 2005 08:29:20 -0700

On Thu, Jul 14, 2005, ?$B9SKR ?$BIp;V wrote:

> >mol = loadPdb water_only_tip5p.pdb
> Loading PDB file: ./water_only_tip5p.pdb
> total atoms in file: 3
> Leap added 2 missing atoms according to residue templates:
> 2 H / lone pairs
> >center mol
> The center is at: 4.92, -0.16, 17.45
> >solvateCap mol TIP3PBOX {4.92, -0.16, 17.45} 10
> Added 112 residues.
> >saveAmberParm mol water_only.crd
> Checking Unit.
> Building topology.
> Building atom parameters.
> For atom: .R<WAT 208>.A<EP1 4> Could not find type: EP
> For atom: .R<WAT 208>.A<EP2 5> Could not find type: EP

First, if you want to use TIP5P water, you will have to load frcmd.tip5p.
Second, you will have to name the tip5p residues as "TP5" (not "WAT") so that
LEaP can figure out which waters are tip5p and which are tip3p. Using the
alias "WAT" is only helpful in the usual case where you have only one type of

[I'm assuming(?) that you have already run test simulations with all of the
waters as tip3p, so you know that everything is working as it should for a
"standard" simulation.]


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Received on Thu Jul 14 2005 - 16:53:00 PDT
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