[gmx-users] problem in simulation with PLP cofactor

Thu Jul 8 12:14:00 CEST 2004

Hi every body
I am facing some problem when i m doing the simulation of protein with 
PLP cofactor. The initial pdb file has connect records for plp with protein. 
But during the simulation PLP is coming out of the protein. 
Is this because the PLP-Protein connection is not defined in gromacs force 
feilds? 
How can this be corrected?

Many- Many thanks in advance.

pankaj kumar. 
PHD student
C/O Dr H.A.Najarajaram
laboratory of computational biology and Bioinformatics
center for dna fingerprinting and diagonistic
nacharam,hyderabad,india
ph.no 91-9848592448

---------REPLY TO-------------
Date:Thu Jul 08 18:00:09 CST 2004
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Subject: gmx-users Digest, Vol 3, Issue 14
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Today's Topics:

   1. Re: Defaults in lipid.itp - please help! (Andreas Kukol)
   2. Re: Defaults in lipid.itp - please help! (Semen Esilevsky)
   3. Re: Defaults in lipid.itp - please help! (Milan Melichercik)

---------------------------------------------------------------------- 

Message: 1
Date: Thu, 08 Jul 2004 10:48:26 +0100
From: "Andreas Kukol" <A.Kukol at warwick.ac.uk>
Subject: Re: [gmx-users] Defaults in lipid.itp - please help!
To: <gmx-users at gromacs.org>
Message-ID: <s0ed267f.091 at liberator.csv.warwick.ac.uk>
Content-Type: text/plain; charset=US-ASCII

It is already included in 3.1.4, otherwise you would not get the error 
message. 
Andreas

>>> yesint4 at yahoo.com 08/07/2004 10:43:40 >>>
Unfortunately we have an old version - 3.1.4 and I'm
not allowed to change the force field files. Is it
another way to do it?

> The parameters of lipid.itp are now included in
> ffgmx.itp. Simply delete #include lipid.itp from the
> topology file of your system.
> 
> Andreas

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Message: 2
Date: Thu, 8 Jul 2004 02:55:41 -0700 (PDT)
From: Semen Esilevsky <yesint4 at yahoo.com>
Subject: Re: [gmx-users] Defaults in lipid.itp - please help!
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <20040708095541.85611.qmail at web40511.mail.yahoo.com>
Content-Type: text/plain; charset=us-ascii

Hear what grompp sais if I remove #include lipid.itp
from my .top file:

Fatal error: Atomtype 'LP3' not found!

--- Andreas Kukol <A.Kukol at warwick.ac.uk> wrote:
> It is already included in 3.1.4, otherwise you would
> not get the error message.
> Andreas
> 
> >>> yesint4 at yahoo.com 08/07/2004 10:43:40 >>>
> Unfortunately we have an old version - 3.1.4 and I'm
> not allowed to change the force field files. Is it
> another way to do it?
> 
> > The parameters of lipid.itp are now included in
> > ffgmx.itp. Simply delete #include lipid.itp from
> the
> > topology file of your system.
> > 
> > Andreas
> 
> 
> 
> 
> 	
> 		
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Message: 3
Date: Thu, 8 Jul 2004 11:56:19 +0200
From: Milan Melichercik <melicher at cray.dbp.fmph.uniba.sk>
Subject: Re: [gmx-users] Defaults in lipid.itp - please help!
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <200407081156.19967.melicher at cray.dbp.fmph.uniba.sk>
Content-Type: text/plain;  charset="utf-8"

On Å t 8. JÃºl 2004 11:43, Semen Esilevsky wrote:
> Unfortunately we have an old version - 3.1.4 and I'm
> not allowed to change the force field files. Is it
> another way to do it?

There is nothing to do with version of Gromacs. If you look into your .top 
file, there you will find line "#include lipid.itp" - simply delete this 
line 
(or make it as comment), cause all information which is imported by this 
command is allready included in forcefield itself.

Milan

>
> > The parameters of lipid.itp are now included in
> > ffgmx.itp. Simply delete #include lipid.itp from the
> > topology file of your system.
> >
> > Andreas
>
> __________________________________
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