[AMBER] how to locate all parameters for specific AA in parm directory

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Fri, 14 Feb 2020 16:41:12 +0900

Dear All,
I want to see the specific parameter values being used in ff14SB for e.g.
for CYS and CYX. Is it possible to print these based on AA type or number?
As per location given here <https://ambermd.org/AmberModels.php>, I am
unable to grep the specific parameters e.g. shown below return no hit.
Please suggest me in understanding/retrieving any specific parameters
(default or loaded) in leap.
Ch 14 of the manual gives related information on printing the whole set of
parameters being used and not based on selected residue-type or number. And
I'm also guessing that it will be in the prmtop format not easily readable
frcmod style.
I want to know what values are being used for bonded (CB-SH), dihedral and
improper and atomic radius terms for all atoms of e.g. CYS and CYX.
Thank you very much for your valuable comments, suggestions and

(base) [exx.c107739 CYP7A1]$ grep S-CB

(base) [exx.c107739 CYP7A1]$ grep C2-S
/usr/local/amber18/dat/leap/parm/frcmod.ff03ua:C2-S 227.0 1.810
changed from 222.0 based on dimethylS nmodes
/usr/local/amber18/dat/leap/parm/frcmod.ff03ua:C2-SH 237.0 1.810
changed from 222.0 based on methanethiol nmodes
/usr/local/amber18/dat/leap/parm/frcmod.ff03ua:C2-C2-S 50.0 114.70
   AA cyx (SCHERAGA JPC 79,1428)
/usr/local/amber18/dat/leap/parm/frcmod.ff03ua:C2-S -C3 62.0 98.90
   AA met
/usr/local/amber18/dat/leap/parm/frcmod.ff03ua:CT-C2-SH 50.0 108.60
   AA cys
/usr/local/amber18/dat/leap/parm/frcmod.ff03ua:C2-SH-HS 43.0 96.00
   changed from 44.0 based on methanethiol nmodes
/usr/local/amber18/dat/leap/parm/frcmod.ff03ua:C2-S -S 68.0 103.70
   AA cyx
/usr/local/amber18/dat/leap/parm/frcmod.ff03ua:CT-C2-S 50.0 114.70
   AA cyx (SCHERAGA JPC 79,1428)
/usr/local/amber18/dat/leap/parm/frcmod.ff03ua:X -C2-S -X 1 0.85
     0.0 3. Yang et al, 2005
/usr/local/amber18/dat/leap/parm/frcmod.ff03ua:X -C2-SH-X 1 0.80
     0.0 3. Yang et al, 2005
/usr/local/amber18/dat/leap/parm/frcmod.ff03ua:C2-S -S -C2 1 3.50
     0.0 -2. JCC,7,(1986),230
/usr/local/amber18/dat/leap/parm/frcmod.ff03ua:C2-S -S -C2 1 0.60
     0.0 3. JCC,7,(1986),230

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
ORCID ID: https://orcid.org/0000-0003-4015-2941
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Received on Fri Feb 14 2020 - 03:30:02 PST
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