Dear All,
We plan to visualize the electrostatic potential map of a pdb (DNA double helix) through PyMol. For this we need to generate the pbsa.phi file using PBSA. We are user of AMBER11 (version 1.4). For this purpose we used the pdb nuc.pdb and also generate the prmtop and inpcrd file. The problems are:
1.no pbsa.phi file was generated
2.we get the following script on the terminal:
segmentation fault
The input used is given below:
pbsa test
&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 we used the following command:
./pbsa -O -i mdin -o mdout -p nuc.top -c nuc.rst
We shall be thankful to know how the pbsa.phi file can be generated.
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Received on Fri Mar 08 2013 - 00:00:02 PST
