[gmx-users] FEP and position restraints

[P]

Right.  Thank you for help.
Now it works fine.
:)
----- Original Message ----- 
From: "Berk Hess" <gmx3 at hotmail.com>
To: <gmx-users at gromacs.org>
Sent: Thursday, April 06, 2006 6:02 PM
Subject: RE: [gmx-users] FEP and position restraints


>
>
>
>>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.
>
>
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