[gmx-users] [Fwd: Regarding Zn problem]
David van der Spoel
spoel at xray.bmc.uu.se
Mon Dec 19 09:26:18 CET 2005
> 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).
Yes but in that case you should use gromos43a1 or gromos56a1 (or OPLS)
> 2. Is it that the simulations done on Gromacs are not publishable.
Of course they are
> 3. You said "referees tend te become more picky about it", so what
> should one do.
The ffgmx force field is a modified gromos87 ff that has not been
described in the literature. Use a newer force field.
> 4. Also I am presently using ffG43a1 forcefield for simulations with
> zinc, is this forcefield
> gives good results or shall I use something else.
This at least avoids the problem of the ill-defined force field
mentioned under 3.
> 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
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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