Dear Jiten,
Thank you so much, I will go ahead as you suggested. its
nice and should work, let you know If I face any error.
Thank God your not near around me or else I would have ask
several questions something like my starting days when I
enetered in Prof. Kim group.
Thanks for everything Jiten. Please convey my regards to
Kolaski.
sincerely,
Odde
--------------------------------------------------------------------------------
> Dear Srinivas,
>
> > NUMBER_REC_GROUPS 1
> > RSTART 1
> > RSTOP 2621
>
>
> Where is the numbering for the crystal water molecules.
> You need to add using RSTART and RSTOP as many as you
> want to define the number of water molecules if they are
> not in order.
>
> Secondly, as I mention before, you do not need parmtop for
> extracting the complex, receptor and ligand coordinates
> from the mdcrd files. What you need most is the proper
> numbering so that when you extract the second coordinate
> it should exactly start from the intital point of the
> second coordinate in the mdcrd file. Otherwise the
> subsequent coordinates will be completely wrong. I think
> the error massage you get for the second coordinate is due
> to this one (check the MM energy in the output file).
> Convert the second crd file to pdb using ambpdb using
> same toplogy file that you have created for this purpose.
> If you see messy coordinate, you need to fix it first with
> proper numbering in your script or you need to correct
> your parmtop. Also remember the new parmtop file and the
> extracted coordinates should contain the same number of
> atoms.
>
> > What do you think? I thought we should make the prmtop
> > files for all of them and the numbering should well
> > match with the MD
>
> Numbering in the new parmtop file will be same only for
> the proteins and ligands. However, it is not important
> factor to consider. Think like this - now you are dealing
> a new set of coordinates defined by the parmtop which
> will represent that new sets of coordinates (no more MD
> coordinates).
>
> If you still have problem please let me know.
>
> Best wishes,
>
> Jiten
> ----- Original Message -----
> From: "odde" <odde.olemiss.edu>
> To: "Jiten" <jiten.postech.ac.kr>
> Sent: Tuesday, April 17, 2007 12:35 AM
> Subject: Re: amber mm-pbsa problem (Need your help jiten)
>
>
> > Thank you so much Jiten,
> > I read your mail twice but I have a small confusion
> > anyway I am attaching the script which I used for
> > extracting the coordinates you will have idea.
> >
> > Extracting coordinates is not the problem it works but
> > the extracted coordinates will be used for further
> > binding energy calculations where I must also specify
> > Receptor.prmtop complex.prmtop and Ligand.prmtop as
> > shown here.
> >
> > May be your right but thought of showing these scripts
> > to you. I will also follow as you suggested and compare
> > the binding energy but please go through this.
> >
> > For extracting coordinates:
> >
> > .GENERAL
> > PREFIX snapshot
> > PATH ./
> > COMPLEX 1
> > RECEPTOR 1
> > LIGAND 1
> > COMPT ./ras-raf.prmtop (Complex)
> > RECPT ./ras.prmtop (receptor)
> > LIGPT ./raf.prmtop (Ligand)
> > GC 1
> > AS 0
> > DC 0
> > MM 0
> > GB 0
> > PB 0
> > MS 0
> > NM 0
> > .MAKECRD
> > BOX YES
> > NTOTAL 42193
> > NSTART 1
> > NSTOP 200
> > NFREQ 1
> > NUMBER_LIG_GROUPS 1
> > LSTART 2622
> > LSTOP 3862
> > NUMBER_REC_GROUPS 1
> > RSTART 1
> > RSTOP 2621
> > .TRAJECTORY
> > TRAJECTORY ./prod1.mdcrd (Trajectory files)
> > TRAJECTORY ./prod2.mdcrd
> > TRAJECTORY ./prod3.mdcrd
> > TRAJECTORY ./prod4.mdcrd
> > .PROGRAMS
> >
> > In order to do binding energy calculations using MM-PBSA
> > method (mm_pbsa.pl script),
> >
> > .GENERAL
> > PREFIX snapshot
> > PATH ./
> > COMPLEX 1
> > RECEPTOR 1
> > LIGAND 1
> > COMPT ./ras-raf.prmtop
> > RECPT ./ras.prmtop
> > LIGPT ./raf.prmtop
> > GC 0
> > AS 0
> > DC 0
> > MM 1
> > GB 1
> > PB 1
> > MS 1
> > NM 0
> > .PB
> > PROC 2
> > REFE 0
> > INDI 1.0
> > EXDI 80.0
> > SCALE 2
> > LINIT 1000
> > PRBRAD 1.4
> > ISTRNG 0.0
> > RADIOPT 0
> > NPOPT 1
> > CAVITY_SURFTEN 0.0072
> > CAVITY_OFFSET 0.00
> > SURFTEN 0.0072
> > SURFOFF 0.00
> > .MM
> > DIELC 1.0
> > .GB
> > IGB 2
> > GBSA 1
> > SALTCON 0.00
> > EXTDIEL 80.0
> > INTDIEL 1.0
> > SURFTEN 0.0072
> > SURFOFF 0.00
> > .MS
> > PROBE 0.0
> > .PROGRAMS
> >
> > What do you think? I thought we should make the prmtop
> > files for all of them and the numbering should well
> > match with the MD
> >
> > If possible, when you find time, kindly have a look at
> > this link to calculate the binding energy calculations.
> >
>
http://amber.scripps.edu/tutorials/advanced/tutorial3/section1.htm
> >
> >
> > Thanks
> >
> > Sincerely,
> > Odde
> >
> >
> > Dr. Srinivas Odde
> > University of Mississippi,
> > Department of Medicinal Chemistry,
> > 417 Faser Hall, University, MS 38677,
> > U. S. A
> > Mobile: 662-801-0772: Lab: 662-915-1853
> > Email: odde.olemiss.edu
> >
> >
> >
> >
> >
>
>
>
>
>
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Received on Wed Apr 18 2007 - 06:07:34 PDT
