Dear community,
I am doing a constant pH simulation of a protein.
I have prepared the necessary files in my system (a desktop) having Amber 9
installed in it while I am running the simulation in a remote cluster having
Amber 10 installed (Don't know the problem might be due to different
version).
Bellow is the procedure I followed while preparing the files necessary for
constant pH simulation
I have change ASP & ASH into AS4, GLU & GLH into GL4 and HIS,HID & HIE into
HIP in my pdb file.
$ tleap
>source leaprc.ff99SB
>set default PBRadii mbondi2
>loadoff constph.lib
>loadamberparm frcmod.constph
>mol=loadpdb my.pdb
>charge mol
Total unperturbed charge: -5.003600
Total perturbed charge: -5.003600
>addions mol Na+ 0
>saveamberparm mol prmtop inpcrd
>quit
Since I am doing the simulation at pH 3 I have exclude TYR and LYS from cpin
file
$ ambpdb -p prmtop <inpcrd | cpinutil.pl -notresname TYR, LYS> cpin
I am sending the input and error files as attachment. Please tell me what is
the problem.
--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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- application/octet-stream attachment: prod.in
Received on Tue Jul 06 2010 - 02:30:04 PDT
