[gmx-users] FEP and position restraints

[Berk Hess]

>From: "P" <pyt1 at op.pl>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: <gmx-users at gromacs.org>
>Subject: [gmx-users] FEP and position restraints
>Date: Thu, 6 Apr 2006 17:52:10 +0200
>
>Hi all
>I'm doing FEP calculation on Zn ions.
>Is three a way to put position restraints
>on perturbated / dummy  atoms.
>When I define in my system.top:
>
>.
>.
>#include "zn.itp"
>[ position_restraints ]
>;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
>
>#include "cl.itp"
>[ position_restraints ]
>;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
>
>#include "dum.itp"
>[ position_restraints ]
>;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
>
>[ system ]
>  ..
>.
>..
>
>
>I'm perturbating Zn ions into dummy atoms.
>  (I'm using ffgmx I've added new DUM atomtype)
>When I use grompp I get following warning:
>
>..
>..
>checking input for internal consistency...
>calling /lib/cpp...
>processing topology...
>Generated 1238 of the 2080 non-bonded parameter combinations
>WARNING 1 [file "system.top", line 11]:
>   No default Position Rest. types for perturbed atoms, using normal values
>WARNING 2 [file "system.top", line 21]:
>   No default Position Rest. types for perturbed atoms, using normal values
>Excluding 3 bonded neighbours for Protein 1
>turning H bonds into constraints...
>..
>..
>
>How can I apply position restraints on them.
>Please give me some comment on this and thank you in advance!!
>All best.

You have already done it.
But as you are doing a free energy calculation,
grompp expect also 3 force constants for the B topology.

Berk.