[AMBER] Electrostatic potential calculation

From: Sudarshan Debnath <sudarshandebnath.ku.rediffmail.com>
Date: 28 Apr 2012 12:13:08 -0000

Dear All,
        I am a user of Amber11. I am trying to generate electrostatic potential surface. Follow the Amber tools11 section 7.3.2. The question is that is it mandatory to neutralize and solvate the system before create prmtop and inpcrd file for electrostatic potential surface calculation in PBSA? When I do this with solvated structure then pbsa.phi is not generated.
I just take a portion of a pdb file (1VJ5.pdb) and create the corresponding prmtop and inpcrd file (no neutralization or salvation). Use the following parameter in input (mdin) file-

PBSA visualization input
&cntrl
ntx=1,
imin=1,
maxcyc=10000,
ipb=1,
inp=0,
/
&pb
npbverb=1,
istrng=0,
epsout=80.0,
epsin=1.0,
space=1.0,
accept=0.001,
sprob=1.4,
cutnb=2,
phiout=1,
phiform=0
/
Then I use the following command

pbsa -O -i mdin -o mdout -p prmtop -c inpcrd

output file and pbsa.phi file is generated. Then I use PyMol (PyMol 1.1eval) windows version and follow the Amber tools11 section 7.3.2. The molecule is loaded by prmtop and inpcrd file. When I write the command-

>load 1VJ5pbsa.phi

PyMol stop working and error message is obtained, this is given below-

Runtime Error!
Program:C:\Program Files(x86)\Delano Scientific\PyMol\PyMol.exe
This application has requested the Runtime to terminate it is an unsual way.

There may be a problem with the 1VJ5pbsa.phi or PyMol. But I can’t understand properly. Please let me know about this problem. I attached prmtop, inpcrd and pbsa.phi file with this mail, please check it.

With best regards,
Sudarshan


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


Received on Sat Apr 28 2012 - 05:30:04 PDT
Custom Search