Dear Amber troupe,
I desperately need your help/suggestions.
We are trying to include C4 terms for Lennard-Jones (12-6-4), using parmed command. However applying the following input file gives zero C4 numbers!!!!
The input is as follows.
-------------------------------------------------
loadRestrt mol.inpcrd
setoverwrite true
add12_6_4 .CR6 c4file c4file.dat polfile lj_1264_pol.dat
outparm mol2.prmtop mol2.inpcrd
printDetails :CR6
printLJMatrix :CR6
quit
Also the C4 values are coming from J. Phys. Chem. Lett. 2017, 8, 5408-5414.
And the file for C4 is as follows.
-------------------
Cr-1.2 180
D+0.7 0
-------------------
The name for the residue in PDB file is CR6. But instead of C4 180 the parmed command generates 0. The command I have applied is:
>>> parmed -p mol.prmtop -c mol.inpcrd -i parmed.in
Does anyone have a clue?
Would you mind please helping me to proceed?
You are so appreciated to consider and help.
Cordially,
/Pooria
Pooria Farahani, PhD Researcher,
Division of Theoretical Chemistry & Biology,
School of Biotechnology, KTH Royal Institute of Technology,
Roslagstullsbacken 15,
SE-10691, Stockholm, Sweden
Cell: +46 707 99 30 69
E-mail: pooriaf.kth.se
https://www.kth.se/profile/pooriaf?l=en
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Received on Tue Jun 12 2018 - 06:00:04 PDT
