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<DIV><FONT size=2><FONT face=宋体><FONT size=2><FONT face=宋体>David van der
Spoel，您好！</FONT> </FONT>
<DIV> </DIV>
<DIV><FONT face=宋体 size=2> </FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=宋体 size=2>======== 2002-12-06 15:43:00 您在来信中写道：
========</FONT></DIV>
<DIV> </DIV>
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<DIV>On Fri, 2002-12-06 at 13:40, Ernesto E. Di Iorio wrote:</DIV>
<DIV>>>
Thanks for your prompt answer, but... I could not find out what is the </DIV>
<DIV>>>
format of the file specbond.dat (I searched in the User's Guide and on the </DIV>
<DIV>>>
web). Could you please tell me what is the meaning of the various terms in </DIV>
<DIV>>> aline?</DIV>
<DIV>>> Thanks, Ernesto</DIV>
<DIV>>>
At 12:14 PM 12/6/02 +0100, you wrote:</DIV>
<DIV>>> >
On Fri, 2002-12-06 at 10:58, Ernesto E. Di Iorio wrote:</DIV>
<DIV>>> > >
Dear gmx users,</DIV>
<DIV>>> > >
I have just installed gromacs and would like to start a simulation on a</DIV>
<DIV>>> > >
protein that contains a FeS4 cluster, namely four cys residues bound to an</DIV>
<DIV>>> > >
Fe atom. In the past I have simulated this protein with gromos96 and I </DIV>
<DIV>>> > have</DIV>
<DIV>>> > >
therefore all the necessary parameters to treat it. My questions are:</DIV>
<DIV>>> > >
1) Can one create a new building block for a new type of Fe, calling it </DIV>
<DIV>>> > say</DIV>
<DIV>>> > > Fe1?</DIV>
<DIV>>> > >
2) Can one generate an own version of ffgmxnb.itp and ffgmxbon.itp?</DIV>
<DIV>>> > >
3) From what I could find out reading the User's Manual and the </DIV>
<DIV>>> > information</DIV>
<DIV>>> > >
on the web, it seems to me that most of the changes in the topology will</DIV>
<DIV>>> > >
have to be done anyhow by hand, is this correct?</DIV>
<DIV>>> > >
I look forward to receiving some tips from you. Should this be of help, I</DIV>
<DIV>>> > >
could send you the gromos96 topology I have used in my previous </DIV>
<DIV>>> > simulations.</DIV>
<DIV>>> >
No, it's quite easy to generate the topology.</DIV>
<DIV>>> >
Just add one line in the file gromacs/share/top/specbond.dat describing</DIV>
<DIV>>> >
the bond between Cys and Fe.</DIV>
<DIV>>> >
Then you ave to add the parameters for S-Fe to the force field files you</DIV>
<DIV>>> >
listed. You can copy those files (take the ffG431a*itp files instead)</DIV>
<DIV>>> >
and put them in your working directory. grompp will use those instead of</DIV>
<DIV>>> > the default ones.</DIV>
<DIV>Here's a sample:</DIV>
<DIV> </DIV>
<DIV>5</DIV>
<DIV>CYS SG 1 CYS SG 1 0.2 CYS2 CYS2</DIV>
<DIV> </DIV>
<DIV>You want to add</DIV>
<DIV>Cys SG 1 FE FE 4 0.2 CYS1 FE</DIV>
<DIV> What is the meaning of 4?</DIV>
<DIV>or something like this, if you have four cysteines bound to the FE and</DIV>
<DIV>0.2 nm is your bondlength.</DIV>
<DIV> </DIV>
<DIV>>> > </DIV>
<DIV>>> > </DIV>
<DIV>>> > --</DIV>
<DIV>>> > Groeten, David.</DIV>
<DIV>>> >
________________________________________________________________________</DIV>
<DIV>>> >
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry</DIV>
<DIV>>> >
Husargatan 3, Box 576, 75123 Uppsala, Sweden</DIV>
<DIV>>> >
phone: 46 18 471 4205 fax: 46 18 511 755</DIV>
<DIV>>> >
spoel@xray.bmc.uu.se spoel@gromacs.org http://xray.bmc.uu.se/~spoel</DIV>
<DIV>>> >
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</DIV>
<DIV>>> >
_______________________________________________</DIV>
<DIV>>> > gmx-users mailing list</DIV>
<DIV>>> > gmx-users@gromacs.org</DIV>
<DIV>>> >
http://www.gromacs.org/mailman/listinfo/gmx-users</DIV>
<DIV>>> >
Please don't post (un)subscribe requests to the list. Use the</DIV>
<DIV>>> >
www interface or send it to gmx-users-request@gromacs.org.</DIV>
<DIV>>> </DIV>
<DIV>>>
-------------------------------------------------------------------</DIV>
<DIV>>> Ernesto E. Di Iorio</DIV>
<DIV>>>
Institute of Biochemistry</DIV>
<DIV>>>
Swiss Federal Institute of Technology</DIV>
<DIV>>> ETH-Hoenggerberg, HPM G9.2</DIV>
<DIV>>> CH-8093 Zurich (Switzerland)</DIV>
<DIV>>>
Phone: +41 1 632 3137 FAX: +41 1 632 1298</DIV>
<DIV>>> </DIV>
<DIV>>>
The first principle is that you must not fool yourself - and you are the </DIV>
<DIV>>>
easiest person to fool. So you have to be very careful about that. After </DIV>
<DIV>>>
you've not fooled yourself, it's easy not to fool other scientists. You </DIV>
<DIV>>>
just have to be honest in a conventional way after that.</DIV>
<DIV>>> (Richard P. Feynman)</DIV>
<DIV>>> </DIV>
<DIV>>>
_______________________________________________</DIV>
<DIV>>> gmx-users mailing list</DIV>
<DIV>>> gmx-users@gromacs.org</DIV>
<DIV>>>
http://www.gromacs.org/mailman/listinfo/gmx-users</DIV>
<DIV>>>
Please don't post (un)subscribe requests to the list. Use the </DIV>
<DIV>>>
www interface or send it to gmx-users-request@gromacs.org.</DIV>
<DIV>>> </DIV>
<DIV>-- </DIV>
<DIV>Groeten, David.</DIV>
<DIV>________________________________________________________________________</DIV>
<DIV>Dr. David van der Spoel,
Biomedical center, Dept. of Biochemistry</DIV>
<DIV>Husargatan 3, Box 576,
75123 Uppsala, Sweden</DIV>
<DIV>phone: 46 18 471 4205
fax: 46 18 511 755</DIV>
<DIV>spoel@xray.bmc.uu.se
spoel@gromacs.org http://xray.bmc.uu.se/~spoel</DIV>
<DIV>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</DIV>
<DIV>_______________________________________________</DIV>
<DIV>gmx-users mailing list</DIV>
<DIV>gmx-users@gromacs.org</DIV>
<DIV>http://www.gromacs.org/mailman/listinfo/gmx-users</DIV>
<DIV>Please don't post (un)subscribe requests to the list. Use the </DIV>
<DIV>www interface or send it to gmx-users-request@gromacs.org.</DIV></BLOCKQUOTE></TD></TR></TBODY></TABLE></FONT></DIV>
<DIV>
<P><FONT face=宋体 size=2>= = = = = = = = = = = = = = = = = = = = = =
</FONT></P>
<P><FONT face=宋体 size=2> 致<BR>礼！</FONT></P>
<DIV><FONT face=宋体 size=2> Weihua Li</FONT></DIV>
<DIV><FONT face=宋体
size=2> <A
href="mailto:whli@mail.shcnc.ac.cn">whli@mail.shcnc.ac.cn</A><BR>
2002-12-07</FONT></FONT></FONT></DIV></DIV></DIV></TD>
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