AMBER Archive (2007)

Subject: RE: AMBER: perturbed atoms are not bonded on using TIP5P water

From: sugino tatsuro (tsugino_at_comas.frsc.tsukuba.ac.jp)
Date: Mon Jan 15 2007 - 21:33:18 CST

Dear David,

Thank you very much for your kind helps. Just before I read your present
e-mail, I sent additional e-mail including more information of my status.
I am very sorry again for your confusing, but I will first attempt what you
told me in your e-mail.

Thank you again.

best wishes,
Sugino

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
David A. Case
Sent: Tuesday, January 16, 2007 11:23 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: perturbed atoms are not bonded on using TIP5P water

On Tue, Jan 16, 2007, sugino tatsuro wrote:
>
> > edit model ( and select a water molecule and set perturbation by GUI )

Although this would seem to make sense, I'm not sure LEaP works that way.

Try something like this (untested!)

source leaprc.ff99SB
loadamberparams frcmod.tip5p
MTP = copy TP5
edit MTP (and make the perturbation changes; check with "desc" that
            the MTP unit has the proper bonds.)
saveoff MTP mtp.off (in case you need it later, or possibly to modify it
                      by hand).

solvatebox MTP TP5 20.0 0.8
saveAmberParm .....
quit

This procedure helps to make sure that the special (perturbed) water uses
parameters different from the regular tip5p water. Just choosing one water
visually to perturb might be getting everything mixed up.

...hope this helps...dac

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