Hello,
I want to calculate the pairwise energy decomposition between the ligand
and every residue within 3 Ang. So I have 2 questions in this regard.
1) how to find ONLY the PROTEIN residues that are within 3 Ang. from the
ligand?
2) how to calculate the pairwise energy decomposition using only pairs that
contain the ligand in order to speed up the calculations?
For 1) I tried to extract the last frame of the trajectory as rst file like
this:
cpptraj -p complex.prmtop
> trajin complex.prod_GB.nc lastframe
> trajout last_frm.rst
> go
> quit
and then use ambmask to find the closest residues like this:
> ambmask -p complex.prmtop -c last_frm.rst -out short -find ":LIG | ((:LIG
> <:3) &
> :ALA,ARG,ASN,ASP,ASD,CYS,GLH,GLN,GLY,HIS,HIP,HIE,HID,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR,VAL)"
> |& grep -A1000 "Condensed format of the atom selection follows:" | awk
> 'NR>1' | perl -p -e "s/\n/ /g" | sed -e 's/://g' | perl -p -e
> "s/([0-9])\s+([0-9])/\1, \2/g"
the above works well for .inpcrd files generated with tleap but not for the
.rst files written by cpptraj. ambmask prints out instead the following:
| New format PARM file being parsed.
> | Version = 1.000 Date = 09/06/16 Time = 16:34:32
> natom = 5633
> nres = 356
> STOP error reading natom from inpcrd
About 2) I have no idea, I just put the closest residues and the ligand
after "print_res=" and MMPBSA.py calculates all pairwise energy
decompositions. If someone knows a faster solution for problems 1) and 2)
please share it on the list.
Thanks in advance for any advice.
Thomas
--
======================================================================
Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Tue Sep 06 2016 - 09:00:03 PDT
