One way to do this might be to build the amino acid alone in leap using the
sequence command, then using parmed to list the parameters in the resulting
prmtop.
On Fri, Feb 14, 2020, 6:12 AM Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
> 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
> clarifications.
>
>
> (base) [exx.c107739 CYP7A1]$ grep S-CB
> /usr/local/amber18/dat/leap/parm/frcmod.ff14SB
>
> (base) [exx.c107739 CYP7A1]$ grep C2-S
> /usr/local/amber18/dat/leap/parm/frcmod.ff*
> /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
>
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
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> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
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>
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>
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>
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Received on Fri Feb 14 2020 - 04:00:01 PST
