AMBER Archive (2009)

Subject: Re: [AMBER] too many undefined parameters in frcmod

From: Junmei Wang (junmwang_at_gmail.com)
Date: Mon Oct 26 2009 - 09:45:04 CDT

Hi Xueqin,
If you want to use both parm99 series force fields and gaff for your organic
molecules (and protein/nucleic acid force field parameters have the higher
priority to be used), a good solution is to merge the protein force field
and the gaff and use the combined force field to run parmchk.

Here is an example:
(1) cp $AMBERHOME/test/antechamber/sustiva/sustiva.mol2 .
(2) atomtype -i sustiva.mol2 -o sustiva.ac -f mol2 -p amber
(3) parmchk -i sustiva.ac -o sustiva.frcmod -f ac -p parm99sb_gaff.dat
(4) parmchk -i sustiva.ac -o sustiva.frcmod2 -f ac -p parm99sb_gaff.dat -a Y
(5) antechamber -fi ac -fo mol2 -j 0 -i sustiva.ac -o sustiva.mol2

Now prepare the leap input
loadamberparams parm99sb_gaff.dat
mymol=loadmol2 sustiva.mol2
loadamberparams sustiva.frcmod
saveamberparm mymol sustiva.prmtop sustiva.prmcrd
quit

As you can see, sustiva.frcmod only has the missing parameters and
sustiva.frcmod2 has all the force field parameters.

I also attached the combined force field parameter file parm99sb_gaff.dat
for your convenience.

Best regards

Junmei

On Thu, Oct 22, 2009 at 6:59 AM, Jason Swails <jason.swails_at_gmail.com>wrote:

> Pang,
> Francois's suggestion should certainly work. However, it looks like you're
> filling in ff99/ff94 parameters using gaff, so it's naming all of the atoms
> for ff99/ff94 (upper-case letters), but it's pulling the parameters from
> gaff.dat (lower-case letters). Another thing you can do is use the '-a'
> flag when you actually run parmchk. This will cause parmchk to print out
> ALL parameters to the frcmod file that you'e creating.
>
> Good luck!
> Jason
>
> On Thu, Oct 22, 2009 at 5:37 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
>
> > Dear Pang xueqin,
> >
> > You could follow two different approaches for your organic structure:
> >
> > 1) You use parm99 FF atom types (with capital letters): you need to load
> > the "parm99.dat" file in LEaP to load all the required FF parameters.
> >
> > source leaprc.ff99SB
> > MOL = loadmol2 YOUR-MOL.mol2
> > saveamberparm MOL MOL.top MOL.crd
> >
> > => LEaP will not save the prmtop/prmcrd files - if missing FF parameters
> > are found, but LEaP will list the missing force field parameters.
> > For instance, you have the CA-HA FF parameters describing the CA-HA bond
> in
> > your frcmod file: This "CA-HA" FF parameters should be in parm99.dat; you
> > should not need to add them in your frcmod file.
> >
> > Then, you create a frcmod file with these missing FF parameters (if LEaP
> > detects missing FF parameters) that you load in a second step:
> >
> > source leaprc.ff99SB
> > FRCMOD = loadamberparams your-frcmod-file
> > MOL = loadmol2 YOUR-MOL.mol2
> > saveamberparm MOL MOL.top MOL.crd
> >
> >
> > 2) You use GAFF FF atom types: you need to use low case FF atom types.
> >
> > Finally, a mol2 file can be used as a prep file: You should not need to
> > create prep file.
> >
> > I hope this helps.
> >
> > regards, Francois
> >
> >
> >
> > I am trying to get a prep field for an organic molecular C16H15N7O2,.
> >> with RED-III according to its tutorial. How every after parmchk, the
> frcmod
> >> give too many undefined parameter.
> >> So, can the prep and frcmod field be used, if not how can I solve this
> >> problem.
> >>
> >> Thank you for your kind help
> >>
> >> Pang xueqin
> >>
> >> Dalian ICP ACS CHINA
> >>
> >> Following are the frcmod for this molecular:
> >> remark goes here
> >> MASS
> >> CA 12.010 0.360 same as c2
> >> HA 1.008 0.135 same as hc
> >> OH 16.000 0.465 same as oh
> >> HO 1.008 0.135 same as ho
> >> CT 12.010 0.878 same as c3
> >> HC 1.008 0.135 same as hc
> >> H1 1.008 0.135 same as hc
> >> N2 14.010 0.530 same as n3
> >> H 1.008 0.161 same as hn
> >> CB 12.010 0.360 same as c2
> >> NA 14.010 0.530 same as na
> >> CR 12.010 0.360 same as c2
> >> C* 12.010 0.360 same as c2
> >> H4 1.008 0.135 same as ha
> >> OS 16.000 0.465 same as os
> >> BOND
> >> CA-HA 344.30 1.087 same as c2-hc
> >> CA-CA 478.40 1.387 same as ca-ca
> >> CA-OH 425.40 1.333 same as c2-oh
> >> OH-HO 369.60 0.974 same as ho-oh
> >> CA-CT 328.30 1.508 same as c2-c3
> >> CT-HC 337.30 1.092 same as c3-hc
> >> CT-CT 303.10 1.535 same as c3-c3
> >> CT-H1 337.30 1.092 same as c3-hc
> >> CT-N2 320.60 1.470 same as c3-n3
> >> N2-H 394.10 1.018 same as hn-n3
> >> N2-CA 449.00 1.364 same as ca-nh
> >> N2-CB 449.00 1.364 same as cc-nh
> >> N2-CR 449.00 1.364 same as cc-nh
> >> N2-NA 426.70 1.420 same as n3-na
> >> NA-H 406.60 1.011 same as hn-na
> >> NA-CR 411.10 1.391 same as c2-na
> >> CR-C* 418.30 1.429 same as cc-cc
> >> C*-C* 418.30 1.429 same as cc-cc
> >> C*-OS 392.60 1.357 same as c2-os
> >> C*-HA 344.30 1.087 same as c2-hc
> >> C*-CA 411.70 1.434 same as ca-cc
> >> CA-H4 344.30 1.087 same as c2-ha
> >> CA-OS 392.60 1.357 same as c2-os
> >> ANGLE
> >> CA-CA-HA 50.300 119.700 same as c2-c2-hc
> >> CA-CA-CA 67.200 119.970 same as ca-ca-ca
> >> CA-CA-CT 64.300 123.420 same as c2-c2-c3
> >> CA-CA-OH 71.600 122.280 same as c2-c2-oh
> >> CA-OH-HO 49.900 108.980 same as c2-oh-ho
> >> CA-CT-HC 47.000 110.490 same as c2-c3-hc
> >> CA-CT-CT 63.700 110.960 same as c2-c3-c3
> >> CT-CT-H1 46.400 110.050 same as c3-c3-hc
> >> CT-CT-N2 66.200 110.380 same as c3-c3-n3
> >> HC-CT-HC 39.400 108.350 same as hc-c3-hc
> >> HC-CT-CT 46.400 110.050 same as c3-c3-hc
> >> CT-N2-H 47.100 109.920 same as c3-n3-hn
> >> CT-N2-CA 62.820 117.790 Calculated with empirical approach
> >> H1-CT-H1 39.400 108.350 same as hc-c3-hc
> >> H1-CT-N2 49.400 109.800 same as hc-c3-n3
> >> N2-CA-N2 71.400 120.980 same as nh-ca-nh
> >> H -N2-CA 49.100 119.380 same as c2-n3-hn
> >> CA-N2-CA 64.300 127.460 same as ca-nh-ca
> >> CA-N2-CB 66.200 124.680 same as c2-n3-c2
> >> CA-N2-NA 66.760 118.340 Calculated with empirical approach
> >> H -N2-H 41.300 107.130 same as hn-n3-hn
> >> N2-CB-N2 72.900 115.960 same as nh-cc-nh
> >> H -N2-CB 49.100 119.380 same as c2-n3-hn
> >> CB-N2-CR 66.200 124.680 same as c2-n3-c2
> >> CB-N2-NA 66.760 118.340 Calculated with empirical approach
> >> N2-CR-NA 73.125 113.900 Calculated with empirical approach
> >> N2-CR-C* 68.600 118.980 same as cc-cc-nh
> >> H -N2-CR 49.100 119.380 same as c2-n3-hn
> >> N2-NA-H 36.098 120.400 Calculated with empirical approach
> >> N2-NA-CR 64.600 124.800 same as c2-na-n3
> >> NA-CR-C* 69.800 121.380 same as c2-c2-na
> >> H -NA-CR 47.600 119.280 same as c2-na-hn
> >> CR-C*-C* 67.900 110.700 same as cc-cc-cc
> >> CR-C*-OS 71.200 121.430 same as c2-c2-os
> >> C*-C*-HA 50.300 119.700 same as c2-c2-hc
> >> C*-C*-C* 67.900 110.700 same as cc-cc-cc
> >> C*-OS-CA 66.000 113.140 same as c2-os-c2
> >> C*-C*-OS 71.200 121.430 same as c2-c2-os
> >> C*-C*-CA 67.700 111.040 same as ca-cc-cc
> >> C*-CA-H4 50.000 120.940 same as c2-c2-ha
> >> C*-CA-OS 71.200 121.430 same as c2-c2-os
> >> HA-C*-CA 50.300 119.700 same as c2-c2-hc
> >> H4-CA-OS 52.400 112.690 same as ha-c2-os
> >> DIHE
> >> CA-CA-CA-OH 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> CA-CA-CA-CA 1 3.625 180.000 2.000 same as X
> >> -ca-ca-X
> >> CA-CA-CA-HA 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> CA-CA-CT-HC 1 0.380 180.000 -3.000 same as
> >> hc-c3-c2-c2
> >> CA-CA-CT-HC 1 1.150 0.000 1.000 same as
> >> hc-c3-c2-c2
> >> CA-CA-CT-CT 1 0.000 0.000 2.000 same as X
> >> -c2-c3-X
> >> HA-CA-CA-HA 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> HA-CA-CA-CT 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> CA-CA-CA-CT 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> CA-CA-OH-HO 1 1.050 180.000 2.000 same as X
> >> -c2-oh-X
> >> HA-CA-CA-OH 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> CA-CT-CT-H1 1 0.156 0.000 3.000 same as X
> >> -c3-c3-X
> >> CA-CT-CT-N2 1 0.156 0.000 3.000 same as X
> >> -c3-c3-X
> >> CT-CT-N2-H 1 0.300 0.000 3.000 same as X
> >> -c3-n3-X
> >> CT-CT-N2-CA 1 0.300 0.000 3.000 same as X
> >> -c3-n3-X
> >> HC-CT-CT-H1 1 0.150 0.000 3.000 same as
> >> hc-c3-c3-hc
> >> HC-CT-CT-N2 1 0.156 0.000 3.000 same as X
> >> -c3-c3-X
> >> CT-N2-CA-N2 1 0.300 180.000 2.000 same as X
> >> -c2-n3-X
> >> H1-CT-N2-H 1 0.300 0.000 3.000 same as X
> >> -c3-n3-X
> >> H1-CT-N2-CA 1 0.300 0.000 3.000 same as X
> >> -c3-n3-X
> >> N2-CA-N2-H 1 0.300 180.000 2.000 same as X
> >> -c2-n3-X
> >> N2-CA-N2-CA 1 1.050 180.000 2.000 same as X
> >> -ca-nh-X
> >> N2-CA-N2-CB 1 1.050 180.000 2.000 same as X
> >> -ca-nh-X
> >> CA-N2-CB-N2 1 1.050 180.000 2.000 same as X
> >> -cc-nh-X
> >> N2-CA-N2-NA 1 0.300 180.000 2.000 same as X
> >> -c2-n3-X
> >> CA-N2-NA-H 1 1.600 0.000 2.000 same as X
> >> -n3-na-X
> >> CA-N2-NA-CR 1 1.600 0.000 2.000 same as X
> >> -n3-na-X
> >> N2-CB-N2-H 1 0.300 180.000 2.000 same as X
> >> -c2-n3-X
> >> N2-CB-N2-CR 1 1.050 180.000 2.000 same as X
> >> -cc-nh-X
> >> N2-CB-N2-NA 1 0.300 180.000 2.000 same as X
> >> -c2-n3-X
> >> CB-N2-CR-NA 1 0.300 180.000 2.000 same as X
> >> -c2-n3-X
> >> CB-N2-CR-C* 1 1.050 180.000 2.000 same as X
> >> -cc-nh-X
> >> CB-N2-NA-H 1 1.600 0.000 2.000 same as X
> >> -n3-na-X
> >> CB-N2-NA-CR 1 1.600 0.000 2.000 same as X
> >> -n3-na-X
> >> N2-CR-NA-N2 1 0.625 180.000 2.000 same as X
> >> -c2-na-X
> >> N2-CR-NA-H 1 0.625 180.000 2.000 same as X
> >> -c2-na-X
> >> N2-CR-C*-C* 1 4.000 180.000 2.000 same as X
> >> -cc-cc-X
> >> N2-CR-C*-OS 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> H -N2-CR-NA 1 0.300 180.000 2.000 same as X
> >> -c2-n3-X
> >> H -N2-CR-C* 1 0.300 180.000 2.000 same as X
> >> -c2-n3-X
> >> N2-NA-CR-C* 1 0.625 180.000 2.000 same as X
> >> -c2-na-X
> >> NA-CR-C*-C* 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> NA-CR-C*-OS 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> H -NA-CR-C* 1 0.625 180.000 2.000 same as X
> >> -c2-na-X
> >> CR-C*-C*-HA 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> CR-C*-C*-C* 1 4.000 180.000 2.000 same as X
> >> -cc-cc-X
> >> CR-C*-OS-CA 1 1.050 180.000 2.000 same as X
> >> -c2-os-X
> >> C*-C*-C*-HA 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> C*-C*-C*-CA 1 4.000 180.000 2.000 same as X
> >> -cc-cc-X
> >> C*-OS-CA-C* 1 1.050 180.000 2.000 same as X
> >> -c2-os-X
> >> C*-OS-CA-H4 1 1.050 180.000 2.000 same as X
> >> -c2-os-X
> >> C*-C*-OS-CA 1 1.050 180.000 2.000 same as X
> >> -c2-os-X
> >> C*-C*-CA-H4 1 4.000 180.000 2.000 same as X
> >> -cc-cc-X
> >> C*-C*-CA-OS 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> HA-C*-C*-OS 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> HA-C*-C*-HA 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> HA-C*-C*-CA 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> C*-C*-C*-OS 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> HA-C*-CA-H4 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> HA-C*-CA-OS 1 6.650 180.000 2.000 same as X
> >> -c2-c2-X
> >> IMPROPER
> >> CA-CA-CA-HA 1.1 180.0 2.0 Using
> default
> >> value
> >> CA-CA-CA-OH 1.1 180.0 2.0 Using
> default
> >> value
> >> CA-CA-CA-CT 1.1 180.0 2.0 Using
> default
> >> value
> >> CA-CT-N2-H 1.1 180.0 2.0 Using
> default
> >> value
> >> N2-N2-CA-N2 1.1 180.0 2.0 Using
> default
> >> value
> >> CA-CA-N2-H 1.1 180.0 2.0 Using
> default
> >> value
> >> CA-H -N2-H 1.1 180.0 2.0 Using
> default
> >> value
> >> CA-CB-N2-H 1.1 180.0 2.0 Using
> default
> >> value
> >> N2-N2-CB-N2 1.1 180.0 2.0 Using
> default
> >> value
> >> CB-CR-N2-H 1.1 180.0 2.0 Using
> default
> >> value
> >> CA-CB-N2-NA 1.1 180.0 2.0 Using
> default
> >> value
> >> CR-H -NA-N2 1.1 180.0 2.0 Using
> default
> >> value
> >> C*-N2-CR-NA 1.1 180.0 2.0 Using
> default
> >> value
> >> C*-CR-C*-OS 1.1 180.0 2.0 Using
> default
> >> value
> >> C*-C*-C*-HA 1.1 180.0 2.0 Using
> default
> >> value
> >> C*-CA-C*-HA 1.1 180.0 2.0 Using
> default
> >> value
> >> C*-H4-CA-OS 1.1 180.0 2.0 Using
> default
> >> value
> >> NONBON
> >> CA 1.9080 0.0860 same as ca
> >> HA 1.4870 0.0157 same as hc
> >> OH 1.7210 0.2104 same as oh
> >> HO 0.0000 0.0000 same as ho
> >> CT 1.9080 0.1094 same as c3
> >> HC 1.4870 0.0157 same as hc
> >> H1 1.4870 0.0157 same as hc
> >> N2 1.8240 0.1700 same as nh
> >> H 0.6000 0.0157 same as hn
> >> CB 1.9080 0.0860 same as cc
> >> NA 1.8240 0.1700 same as na
> >> CR 1.9080 0.0860 same as cc
> >> C* 1.9080 0.0860 same as cc
> >> H4 1.4870 0.0157 same as hc
> >> OS 1.6837 0.1700 same as os
> >>
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



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