I admit to being confused now. parmchk2 is designed to let you know which
force field parameters you will need for a molecule, and make guesses about
them if needed.
Are you trying to find out which force field parameters were actually used
in the prmtop, or which ones you might be missing?
The force field that is included in a prmtop only comes from the parameter
files you give to leap when building it.
you originally said " 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."
parmed will do exactly this. It will show you the parameters being used for
specific (or all) atoms. Look at the parmed "print" commands (type help
inside parmed). Your other options is to look inside the relevant parameter
files in $AMBERHOME/dat/leap/ directories. You will first need to find out
the atom types for the atoms of interest, and then trace to find the
combinations in the bond etc sections. Parmed does this for you and is much
easier to use in my opinion.
On Fri, Feb 14, 2020 at 11:22 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Dear Prof. Carlos Simerling and other experts,
> The sequence command gives expected data, but it is not easily readable
> especially for larger non-standard residues.
> The frcmod format written by the pramchk2 has the atom-type based
> parameters which I find easy to read.
>
> But I'm unable to confirm from the manual (15.1.2) if parmchk2 can be used
> for extracting standard AA parameters since there isn't any option to
> control the frcmod.ff file choice from which the parameters are being read
> (does it read gaff files only?). Thus I don't know if the parameters in
> the earlier email are from which parameter set from among those available
> in the dat/leap folder.
>
> Please suggest on these aspects and if my approach is sensible enough
> considering the possibility that parameter values from different sets might
> get mixed up here (e.g. some values from ff14SB and some from ff12SB set or
> other combinations)
> Thank you and best regards
>
> On Fri, Feb 14, 2020 at 2:08 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
>
> > I tried by running parmchk2 on mol2 files for CYS and CYX and generated
> > the frcmod.
> > These reads the following. For CYS this look OK, but for CYX some
> > parameters are missing.
> > Isn't it expected to find all CYX parameters also, or I misunderstood
> > something here?
> > I will also try Carlos's suggestion soon.
> >
> > *CYS frcmod*
> > Remark line goes here
> > MASS
> > N 14.010 0.530 same as n
> > H 1.008 0.161 same as hn
> > CT 12.010 0.878 same as c3
> > H1 1.008 0.135 same as h1
> > SH 32.060 2.900 same as sh
> > C 12.010 0.616 same as c
> > O 16.000 0.434 same as o
> >
> > BOND
> > H -N 403.20 1.013 same as hn- n, penalty score= 0.0
> > CT-N 328.70 1.462 same as c3- n, penalty score= 0.0
> > CT-H1 330.60 1.097 same as c3-h1, penalty score= 0.0
> > CT-CT 300.90 1.538 same as c3-c3, penalty score= 0.0
> > C -CT 313.00 1.524 same as c-c3, penalty score= 0.0
> > CT-SH 213.70 1.843 same as c3-sh, penalty score= 0.0
> > C -O 637.70 1.218 same as c- o, penalty score= 0.0
> >
> > ANGLE
> > H1-CT-N 49.800 108.880 same as h1-c3-n , penalty score= 0.0
> > CT-CT-N 65.900 111.610 same as c3-c3-n , penalty score= 0.0
> > C -CT-N 67.000 109.060 same as c -c3-n , penalty score= 0.0
> > CT-N -H 45.800 117.680 same as c3-n -hn, penalty score= 0.0
> > CT-CT-H1 46.400 109.560 same as c3-c3-h1, penalty score= 0.0
> > CT-CT-SH 60.400 113.130 same as c3-c3-sh, penalty score= 0.0
> > CT-C -O 67.400 123.200 same as c3-c -o , penalty score= 0.0
> > C -CT-H1 47.000 108.220 same as c -c3-h1, penalty score= 0.0
> > C -CT-CT 63.300 111.040 same as c -c3-c3, penalty score= 0.0
> > H1-CT-H1 39.200 108.460 same as h1-c3-h1, penalty score= 0.0
> > H1-CT-SH 42.000 108.420 same as h1-c3-sh, penalty score= 0.0
> >
> > DIHE
> > H1-CT-CT-N 9 1.400 0.000 3.000 same as X
> > -c3-c3-X , penalty score= 0.0
> > N -CT-CT-SH 9 1.400 0.000 3.000 same as X
> > -c3-c3-X , penalty score= 0.0
> > O -C -CT-N 6 0.000 180.000 2.000 same as X -c
> > -c3-X , penalty score= 0.0
> > H1-CT-N -H 6 0.000 0.000 2.000 same as X
> > -c3-n -X , penalty score= 0.0
> > CT-CT-N -H 6 0.000 0.000 2.000 same as X
> > -c3-n -X , penalty score= 0.0
> > C -CT-N -H 6 0.000 0.000 2.000 same as X
> > -c3-n -X , penalty score= 0.0
> > H1-CT-CT-H1 9 1.400 0.000 3.000 same as X
> > -c3-c3-X , penalty score= 0.0
> > H1-CT-CT-SH 9 1.400 0.000 3.000 same as X
> > -c3-c3-X , penalty score= 0.0
> > O -C -CT-H1 1 0.800 0.000 -1.000 same as
> > h1-c3-c -o
> > O -C -CT-H1 1 0.000 0.000 -2.000 same as
> > h1-c3-c -o
> > O -C -CT-H1 1 0.080 180.000 3.000 same as
> > h1-c3-c -o , penalty score= 0.0
> > O -C -CT-CT 6 0.000 180.000 2.000 same as X -c
> > -c3-X , penalty score= 0.0
> > C -CT-CT-H1 9 1.400 0.000 3.000 same as X
> > -c3-c3-X , penalty score= 0.0
> > C -CT-CT-SH 9 1.400 0.000 3.000 same as X
> > -c3-c3-X , penalty score= 0.0
> >
> > IMPROPER
> >
> > NONBON
> > N 1.8240 0.1700 same as n
> > H 0.6000 0.0157 same as hn
> > CT 1.9080 0.1094 same as c3
> > H1 1.3870 0.0157 same as h1
> > SH 2.0000 0.2500 same as sh
> > C 1.9080 0.0860 same as c
> > O 1.6612 0.2100 same as o
> >
> >
> > *CYX frcmod*
> > Remark line goes here
> > MASS
> > N 14.010 0.530 same as n
> > H 1.008 0.161 same as hn
> > CT 12.010 0.878 same as c3
> > S 32.060 2.900 same as ss
> > C 12.010 0.616 same as c
> > O 16.000 0.434 same as o
> >
> > BOND
> > H -N 403.20 1.013 same as hn- n, penalty score= 0.0
> > CT-N 328.70 1.462 same as c3- n, penalty score= 0.0
> > CT-H 0.00 0.000 ATTN, need revision
> > CT-CT 300.90 1.538 same as c3-c3, penalty score= 0.0
> > C -CT 313.00 1.524 same as c-c3, penalty score= 0.0
> > CT-S 215.90 1.839 same as c3-ss, penalty score= 0.0
> > C -O 637.70 1.218 same as c- o, penalty score= 0.0
> >
> > ANGLE
> > H -CT-N 0.000 0.000 ATTN, need revision
> > CT-CT-N 65.900 111.610 same as c3-c3-n , penalty score= 0.0
> > C -CT-N 67.000 109.060 same as c -c3-n , penalty score= 0.0
> > CT-N -H 45.800 117.680 same as c3-n -hn, penalty score= 0.0
> > CT-CT-H 0.000 0.000 ATTN, need revision
> > CT-CT-S 61.300 110.270 same as c3-c3-ss, penalty score= 0.0
> > CT-C -O 67.400 123.200 same as c3-c -o , penalty score= 0.0
> > C -CT-H 0.000 0.000 ATTN, need revision
> > C -CT-CT 63.300 111.040 same as c -c3-c3, penalty score= 0.0
> > H -CT-H 0.000 0.000 ATTN, need revision
> > H -CT-S 0.000 0.000 ATTN, need revision
> >
> > DIHE
> > H -CT-CT-N 9 1.400 0.000 3.000 same as X
> > -c3-c3-X , penalty score= 0.0
> > N -CT-CT-S 9 1.400 0.000 3.000 same as X
> > -c3-c3-X , penalty score= 0.0
> > O -C -CT-N 6 0.000 180.000 2.000 same as X -c
> > -c3-X , penalty score= 0.0
> > H -CT-N -H 6 0.000 0.000 2.000 same as X
> > -c3-n -X , penalty score= 0.0
> > CT-CT-N -H 6 0.000 0.000 2.000 same as X
> > -c3-n -X , penalty score= 0.0
> > C -CT-N -H 6 0.000 0.000 2.000 same as X
> > -c3-n -X , penalty score= 0.0
> > H -CT-CT-H 9 1.400 0.000 3.000 same as X
> > -c3-c3-X , penalty score= 0.0
> > H -CT-CT-S 9 1.400 0.000 3.000 same as X
> > -c3-c3-X , penalty score= 0.0
> > O -C -CT-H 6 0.000 180.000 2.000 same as X -c
> > -c3-X , penalty score= 0.0
> > O -C -CT-CT 6 0.000 180.000 2.000 same as X -c
> > -c3-X , penalty score= 0.0
> > C -CT-CT-H 9 1.400 0.000 3.000 same as X
> > -c3-c3-X , penalty score= 0.0
> > C -CT-CT-S 9 1.400 0.000 3.000 same as X
> > -c3-c3-X , penalty score= 0.0
> >
> > IMPROPER
> >
> > NONBON
> > N 1.8240 0.1700 same as n
> > H 0.6000 0.0157 same as hn
> > CT 1.9080 0.1094 same as c3
> > S 2.0000 0.2500 same as ss
> > C 1.9080 0.0860 same as c
> > O 1.6612 0.2100 same as o
> >
> >
> >
> >
> > On Fri, Feb 14, 2020 at 8:31 PM Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> >> 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,
> >> > ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> >> > Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> >> > VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> >> > India.
> >> > Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> >> > Email: vaibhav.dixit.pilani.bits-pilani.ac.in,
> vaibhavadixit.gmail.com
> >> > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> >> > https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> >> >
> >> > ORCID ID: https://orcid.org/0000-0003-4015-2941
> >> >
> >> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >> >
> >> > P Please consider the environment before printing this e-mail
> >> > _______________________________________________
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> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > --
> >
> > 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,
> > ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> > Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> > VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> > India.
> > Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> > Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> > https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> >
> > ORCID ID: https://orcid.org/0000-0003-4015-2941
> >
> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >
> > P Please consider the environment before printing this e-mail
> >
> >
>
> --
>
> 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,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> P Please consider the environment before printing this e-mail
> _______________________________________________
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Received on Fri Feb 14 2020 - 09:00:02 PST
