[gmx-users] [Fwd: Regarding Zn problem]

David van der Spoel spoel at xray.bmc.uu.se
Mon Dec 19 08:46:59 CET 2005

-------- Original Message --------
Subject: Regarding Zn problem
Date: Mon, 19 Dec 2005 10:36:31 +0530 (IST)
From: Kirti Patel <kirti at chem.iitb.ac.in>
To: spoel at xray.bmc.uu.se

Dear David,

I am new to gromcas and am working on designing Zinc peptides with 
stereochemistry as a variable.

In the following mail to gromacs userlist you mentioned about using new 
forcefield for publishing
the results.

could you please mention me in details for these.

1. Why should we use new force field when we have already a recognised 
force field (Gromos).

2. Is it that the simulations done on Gromacs are not publishable.

3. You said "referees tend te become more picky about it", so what 
should one do.

4. Also I am presently using ffG43a1 forcefield for simulations with 
zinc, is this forcefield
gives good results or shall I use something else.

Waiting for your answer.

Thanks in advance.

Kirti Patel

Message: 5
Date: Sun, 18 Dec 2005 10:40:45 +0100
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] Zn problem
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <43A52E9D.4020306 at xray.bmc.uu.se>
Content-Type: text/plain; charset=UTF-8; format=flowed

hnam wrote:
> In the name of God
> Hello Gromacs users
> I work on adenosine deaminase (ADA). ADA has Zn in its active site and it
> connect to three his and one asp. When I make
> itp file by pdb2gmx , it makes two itp files ,one of them is for
protein and
> another is for Zn .
> I combined this two itps to one itp file and defined new atom types and
> his and asp (that are connected to ZN) and also I inserted new
parameters in
> ffgmxbon.itp  and ffgmxbn.itp and aminoaside.dat and ffgmx.rtp and
> library but when I run grompp it says: fatal error :"no such molecule
> protein "  and source code file :toppush.c line 1264 .Would you please
> me everything that I must do.

Check chapter 5 in the manual You have mixed up the order of entries in
the files. You also should use a newer force field if you want to
publish results (referees tend te become more picky about it ).

> Thank you very much in advance
> Institute of  Biochemistry  and  Biophysics (IBB)
> Tehran University
> P.O.box 1417614411
> Tehran
> Iran

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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