AMBER Archive (2009)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Oct 22 2009 - 04:37:46 CDT


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

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