RE: AMBER: how to solvate in TIP5P box

From: Ross Walker <>
Date: Wed, 26 Jan 2005 10:26:22 -0800

Dear Yi,

> I'd like to solvate my peptide in TIP5P box. I loaded the
> frcmod.tip5p,
> but I cannot find the TIP5PBOX to solvate it. There're only
> TIP3PBOX and
> TIP4PBOX. What should I do? Thanks!

Loading the frcmod.tip5p just loads the parameters for the tip5p atom types.
It does not define the TIP5P unit. However, tip5p is defined in the default
solvents.lib file which should be loaded by leap automatically if you used
one of the leaprc.ffxx files.

This only defines a single molecule of water called TP5 and not a box. The
difference is not too important. The TIPXPBOX's are just pre-equilibrated
water boxes.


solvatebox myunit TP5 10

Should serve to add a 10 angstrom buffer of TP5 water around your unit. Just
be aware that this system may need slightly longer to equilibrate than
solvating with a pre-equilibrated water unit.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Wed Jan 26 2005 - 18:53:00 PST
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