[gmx-users] Zn problem

[David van der Spoel]

hnam wrote:
> In the name of Allah
> Hello Dr.David van der Spoel 
> Thank you very much for your kindness.
> I don't understand your purpose of   "order of entries in the files" .
That is described in the manual.

> Will you please explain what i must do.
> Thank you very much in advance

If you modify the rtp files etc. you will have to rerun pdb2gmx. If you 
want the Zn to be bonded covalently to the His and Asp you will also 
have to edit the specbond.dat file (check mailing list archives).


> Institute of  Biochemistry  and  Biophysics (IBB)
> Tehran University 
> P.O.box 1417614411
> Tehran 
> Iran 
> Thank you very much in advance
> Institute of  Biochemistry  and  Biophysics (IBB)
> Tehran University 
> P.O.box 1417614411
> Tehran 
> Iran 
> 
> 
> 
> -----Original Message-----
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Sun, 18 Dec 2005 10:40:45 +0100
> Subject: Re: [gmx-users] Zn problem
> 
> 
>>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 new 
>>
>>>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
>>
>>ffgmx.atp 
>>
>>>library but when I run grompp it says: fatal error :"no such molecule
>>
>>type 
>>
>>>protein "  and source code file :toppush.c line 1264 .Would you
>>
>>please tell 
>>
>>>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 
>>>
>>>
>>>_______________________________________________
>>>gmx-users mailing list
>>>gmx-users at gromacs.org
>>>http://www.gromacs.org/mailman/listinfo/gmx-users
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>>>www interface or send it to gmx-users-request at gromacs.org.
>>
>>
>>-- 
>>David.
>>_______________________________________________________________________
>>_
>>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
>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>+
>>_______________________________________________
>>gmx-users mailing list
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> 
> 
> 
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-- 
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++