Re: AMBER: doubts with a new aminoacid

From: David A. Case <>
Date: Tue, 1 Feb 2005 15:35:36 -0800

On Tue, Feb 01, 2005, Gustavo Pierdominici Sottile wrote:

> I use the keyword desc, the following message appears
> if the aminoacid is the new one:
> No improper torsions
> Contents:
> But if it is any standard aminoacid, the message is this:
> Improper torsions:
> Contents:
> In none of them the list of improper torsions appears, but in standard ones
> the message is different from the new one. I have already generate the file
> to recognize this new aminoacid following the structure that have the other
> ones. One part of this file is:
> CG CD2
> CE2 CD2

You need a blank line between the LOOP section and the IMPROPER section
(that is, right here).

> -M CA N H
> CA +M C O
> CD1 CE2 NE1 HE1
> CE2 CH2 CZ2 OZ2
> CZ2 CZ3 CH2 NH2
> CH2 CE3 CZ3 HZ3
> CG NE1 CD1 HD1

However, LEaP ignores any improper torsions specified in the prep files.
You should use rdparm to examine a prmtop file that contains this new residue,
to make sure that you are getting the terms you want.

> Another doubt is that when writing check, the following warning appears, and
> I don?t understand it
> WARNING: The unperturbed charge of the unit: -27.000000 is not zero.

This means that the sum of charges on the atoms in this unit is -27. If that
is the correct value, fine. If not, you will need to look at the charges
to try to find out where the problem is.

> Finally I would like to know if it is posible to change one specifyc van der
> Walls interation. This is because I have defined a new atom type CS with the
> same VDW parameters as CT (Ri 1.908 ei 0.1094). The VDW between CS and H1
> (Rj 1.487 ej 0.086) is calculated obtaining VDW well depth Rij= Ri+ Rj and
> eij= (ei*ej)**1/2. I need to change these parameters for this specifyc
> interaction. Is it possible?

It's not possible through any standard user interface element. You could
hand-edit the prmtop file to make such a change: find the Lennard Jones A and
C parameters that correpond to the pair you want to change, and edit them to
whatever values you wish.

....good luck...dac

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Received on Tue Feb 01 2005 - 23:53:00 PST
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