Hi,
Only one topology file is needed...
On Sun, May 9, 2010 at 2:50 AM, geyan <geyan.big.ac.cn> wrote:
> Thanks for your help,Bill.
> One more point,if the value of the NUMBER_REC_GROUPS is 2,do I need to
> produce the two separate topology files that corresponding to the two
> receptor parts or just with one single topology file that contain both of
> the two?
>
>
>
> 2010-05-09
>
>
>
> geyan
>
>
>
> 发件人： Bill Miller III
> 发送时间： 2010-05-09 11:15:01
> 收件人： AMBER Mailing List
> 抄送：
> 主题： Re: [AMBER] About MM-PBSA's extracting coordinate scirpt
> Assuming you have set up your receptor and ligand topology files as you
> have
> described you should be able to list the ligand as you have already
> described and then describe the receptor mask like this:
> NUMBER_REC_GROUPS 2
> RSTART 1
> RSTOP 10
> RSTART 41
> RSTOP 100
> This is how I understand it based on the descriptions in the manual for
> this
> section.
> As a side note, you could do this calculation using MMPBSA.py by supplying
> the correct topology files, then the receptor and ligand masks would be
> guessed by the script without the user needing to input start and stop atom
> numbers or residues for either molecule. Just an idea.
> Good luck!
> -Bill
> On Sat, May 8, 2010 at 12:15 PM, geyan <geyan.big.ac.cn> wrote:
> > hello every Amber-user,
> > I have simulated a complex composed of three moleculares of protein and
> > one molecular of DNA.Now I got the complex's trajectory and want to
> > calculate each protein's contribution to the total binding energy of the
> > interaction of the proteins and DNA.
> > Now the question is how to set the parameters of the MM_PBSA tutorial's
> > extracting coordinate script.Specially speaking,I don't know how to deal
> > with the
> > NUMBER_LIG_GROUPS and the NUMBER_REC_GROUPS.In my opinion,as I want to
> > calculate the single protein's contribution,I have to set this very
> protein
> > to receptor or ligand,and let the remains to be the ligand or
> receptor.For
> > example,if my complex has 100 atoms totally and composed like
> this:DNA:1-10
> > atom,protein A:11-40 atom,protein B:41-70,protein C:71-100.If now I want
> to
> > konw the detailed contribution of protein A,so in the NUMBER_LIG_GROUPS
> > item,I can set it like this,
> > NUMBER_LIG_GROUPS 1
> > LSTART 11
> > LSTOP 40
> > now,the question appears,that is how to deal with the NUMBER_REC_GROUPS
> > item.The remained moleculars is not single one and the atoms are
> obviously
> > not consecutive.So does anybody know how to figure it out?
> > Many thanks!
> > 2010-05-08
> >
> >
> >
> > geyan
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Sun May 09 2010 - 00:30:03 PDT
