[AMBER] too many undefined parameters in frcmod

From: xueqin pang <pangxueqintea.yahoo.com.cn>
Date: Thu, 22 Oct 2009 16:52:57 +0800 (CST)

Hello everyone,
 
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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Received on Thu Oct 22 2009 - 02:00:03 PDT
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