AMBER Archive (2005)

Subject: Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth

From: Petr Kulhanek (kulhanek_at_chemi.muni.cz)
Date: Thu Apr 28 2005 - 02:02:47 CDT

Hello,

>I am thinking that the reason for this difference lies in the perturbation
>I am intended. In one case (meth->eth), I am changing a proton to a
>carbon, and in another one (eth->meth), I am changing a carbon to a
>proton. This might be the reason why I am getting such a difference.
>(Maybe the method I am following is no good for creating/annihilating
>heavy atoms) So, I will test my 'new' sander to a case where I am
>creating/annihilating just protons.
>
I have one remark related to your problem. Format of AMBER topology is
not able to reflect mass changes in perturbation calculations. It means
that if you change a carbon to a proton, only force field parameters
(bond lengths, ...) are changed but mass not. This could be the
explanation of observed differences. To solve this problem, you should
use dummy atoms.

Petr Kulhanek

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