AMBER Archive (2004)

Subject: Re: AMBER: Questions about pert.charge and atom type change.

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Wed Jun 30 2004 - 19:54:28 CDT

As was pointed out in previous emails, in amber7 you need to specify the
charge of the target state. But this is changed since amber8 to the
charge difference between source and target.

Yes, you need to perturb both OH and HO to SH and HS respectively. You
should have all the charges for both states.

Guanglei

Chunhu Tan wrote:

> Hi, all,
>
> I am trying to do TI with sander, but I am still confused with the
> pert.charge
> in xleap. My question is, when a H (with the charge 0.0791) atom becomes a
> dummy, if
> its pert.charge is 0-0.0791=-0.0791? If this is true, why the dummy H atoms
> on
> this page have no pert.charge?
> http://web.njit.edu/all_topics/Prog_Lang_Docs/html/amber7/gibbs_box/HTML/xleap_edit_selected.html
> Also on this page, the first CT's charge, in VAL, is 0.2985, in ALA,
> is -0.1825, so its pert.charge
> should be -0.1825-0.2985=0.4810, not the 0.105, am I right?
>
> Another question. When I perturbed CH3-OH to CH3-SH, if both the O
> atom(type OH) and the H
> atom attached to it (type HO) should be changed to type SH and HS
> respectively? I tried to only
> change the O, but when I saveamberparmpert, LEap told me :
> No bond parameter for: SH-HO
> Can't find angle parameter: CT-SH-HO
> When I also changed the H, it is OK, but I am not sure it is right, and what
> about the pert.charge of H?
>
> Thanks in advance!!
>
>
>
>
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