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 - 06:07:23 PDT
