[gmx-users] FeS4 cluster

[Weihua Li]

David van der Spoel，您好！  

　　

======== 2002-12-06 15:43:00 您在来信中写道： ========

On Fri, 2002-12-06 at 13:40, Ernesto E. Di Iorio wrote:
>>  Thanks for your prompt answer, but... I could not find out what is the 
>>  format of the file specbond.dat (I searched in the User's Guide and on the 
>>  web). Could you please tell me what is the meaning of the various terms in 
>>  aline?
>>  Thanks, Ernesto
>>  At 12:14 PM 12/6/02 +0100, you wrote:
>>  > On Fri, 2002-12-06 at 10:58, Ernesto E. Di Iorio wrote:
>>  >  >  Dear gmx users,
>>  >  >  I have just installed gromacs and would like to start a simulation on a
>>  >  >  protein that contains a FeS4 cluster, namely four cys residues bound to an
>>  >  >  Fe atom. In the past I have simulated this protein with gromos96 and I 
>>  >  have
>>  >  >  therefore all the necessary parameters to treat it. My questions are:
>>  >  >  1) Can one create a new building block for a new type of Fe, calling it 
>>  >  say
>>  >  >  Fe1?
>>  >  >  2) Can one generate an own version of ffgmxnb.itp and ffgmxbon.itp?
>>  >  >  3) From what I could find out reading the User's Manual and the 
>>  >  information
>>  >  >  on the web, it seems to me that most of the changes in the topology will
>>  >  >  have to be done anyhow by hand, is this correct?
>>  >  >  I look forward to receiving some tips from you. Should this be of help, I
>>  >  >  could send you the gromos96 topology I have used in my previous 
>>  >  simulations.
>>  > No, it's quite easy to generate the topology.
>>  > Just add one line in the file gromacs/share/top/specbond.dat describing
>>  > the bond between Cys and Fe.
>>  > Then you ave to add the parameters for S-Fe to the force field files you
>>  > listed. You can copy those files (take the ffG431a*itp files instead)
>>  > and put them in your working directory. grompp will use those instead of
>>  > the default ones.
Here's a sample:

5
CYS     SG      1       CYS     SG      1       0.2     CYS2    CYS2

You want to add
Cys SG 1 FE FE 4 0.2 CYS1 FE
 What is the meaning of 4?
or something like this, if you have four cysteines bound to the FE and
0.2 nm is your bondlength.

>>  > 
>>  > 
>>  > --
>>  > Groeten, David.
>>  > ________________________________________________________________________
>>  > Dr. David van der Spoel,        Biomedical center, Dept. of Biochemistry
>>  > Husargatan 3, Box 576,          75123 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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>>  
>>  -------------------------------------------------------------------
>>  Ernesto E. Di Iorio
>>  Institute of  Biochemistry
>>  Swiss Federal Institute of Technology
>>  ETH-Hoenggerberg, HPM G9.2
>>  CH-8093 Zurich (Switzerland)
>>  Phone: +41 1 632 3137  FAX: +41 1 632 1298
>>  
>>  The first principle is that you must not fool yourself - and you are the 
>>  easiest person to fool. So you have to be very careful about that. After 
>>  you've not fooled yourself, it's easy not to fool other scientists. You 
>>  just have to be honest in a conventional way after that.
>>  (Richard P. Feynman)
>>  
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel,  Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,   75123 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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= = = = = = = = = = = = = = = = = = = = = = 
　　　　　　　　致
礼！
　　　　　　　　　　　　　　Weihua Li
                          whli at mail.shcnc.ac.cn
　　　　　　　　　　 　　　　　2002-12-07 
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