Dear all,
As sqm was giving high penalty scores for one of the ligands, I had
followed these steps to process the same through gaussian -
- Added hydrogens to LIG_docked... using chimera and named it as LIG.pdb
$antechamber -fi pdb -fo gcrt -i LIG.pdb -o LIG.gau
$g09 <LIG.gau> LIG.out
$antechamber -i LIG.out -fi gout -o LIG.prepi -fo prepi -c resp -eq 1 -nc 0
-s 0 -at amber
$parmchk2 -i LIG.prepi -f prepi -o LIG.frcmod
====
The output file (LIG.frcmod) still has the penalty scores -
Remark line goes here
MASS
N 14.010 0.530 same as n
H 1.008 0.161 same as hn
C 12.010 0.616 same as c
O 16.000 0.434 same as o
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 h1
CA 12.010 0.360 same as ca
C* 12.010 0.360 same as cc
HA 1.008 0.135 same as ha
CB 12.010 0.360 same as ca
S 32.060 2.900 same as ss
BOND
H -N 403.20 1.013 same as hn- n, penalty score= 0.0
C -N 427.60 1.379 same as c- n, penalty score= 0.0
C -O 637.70 1.218 same as c- o, penalty score= 0.0
N -OH 400.20 1.406 same as n-oh, penalty score= 0.0
CT-N 328.70 1.462 same as c3- n, penalty score= 0.0
HO-OH 371.40 0.973 same as ho-oh, penalty score= 0.0
CT-CT 300.90 1.538 same as c3-c3, penalty score= 0.0
CT-H1 330.60 1.097 same as c3-h1, penalty score= 0.0
CA-CT 321.00 1.516 same as c3-ca, penalty score= 0.0
CT-HC 330.60 1.097 same as c3-hc, penalty score= 0.0
C*-CA 385.10 1.456 same as ca-cc, penalty score= 0.0
CA-S 249.80 1.781 same as ca-ss, penalty score= 0.0
C*-HA 349.10 1.084 same as cc-ha, penalty score= 0.0
C*-CB 385.10 1.456 same as ca-cc, penalty score= 0.0
CA-CB 461.10 1.398 same as ca-ca, penalty score= 0.0
CB-CB 461.10 1.398 same as ca-ca, penalty score= 0.0
CA-HA 345.80 1.086 same as ca-ha, penalty score= 0.0
CA-CA 461.10 1.398 same as ca-ca, penalty score= 0.0
CB-S 249.80 1.781 same as ca-ss, penalty score= 0.0
ANGLE
N -C -O 74.220 123.050 same as n -c -o , penalty score= 0.0
N -C -N 72.900 113.560 same as n -c -n , penalty score= 0.0
H -N -H 39.560 117.950 same as hn-n -hn, penalty score= 0.0
C -N -H 48.330 117.550 same as c -n -hn, penalty score= 0.0
C -N -OH 68.210 115.510 same as c -n -oh, penalty score= 0.0
C -N -CT 63.390 120.690 same as c -n -c3, penalty score= 0.0
HO-OH-N 50.520 101.290 same as ho-oh-n , penalty score= 0.0
CT-CT-N 65.910 111.610 same as c3-c3-n , penalty score= 0.0
H1-CT-N 49.840 108.880 same as h1-c3-n , penalty score= 0.0
CA-CT-N 66.210 112.380 same as ca-c3-n , penalty score= 0.0
CT-N -OH 66.930 112.970 same as c3-n -oh, penalty score= 0.0
CT-CT-HC 46.340 109.800 same as c3-c3-hc, penalty score= 0.0
C*-CA-CT 63.530 120.770 same as c3-ca-ca, penalty score= 2.0
CT-CA-S 61.417 115.975 Calculated using c3-ca-ss, penalty score=
0.0
CT-CT-H1 46.390 109.560 same as c3-c3-h1, penalty score= 0.0
CA-CT-CT 63.150 112.070 same as c3-c3-ca, penalty score= 0.0
HC-CT-HC 39.400 107.580 same as hc-c3-hc, penalty score= 0.0
CA-CT-H1 46.990 109.560 same as ca-c3-h1, penalty score= 0.0
CA-C*-HA 45.830 124.040 same as ca-cc-ha, penalty score= 0.0
CA-C*-CB 63.240 122.940 same as ca-cc-ca, penalty score= 0.0
CA-S -CB 62.350 98.830 same as ca-ss-ca, penalty score= 0.0
C*-CA-S 61.600 120.060 same as ca-ca-ss, penalty score= 2.0
C*-CB-CA 65.020 120.790 same as ca-ca-cc, penalty score= 0.0
C*-CB-CB 65.020 120.790 same as ca-ca-cc, penalty score= 0.0
CB-C*-HA 45.830 124.040 same as ca-cc-ha, penalty score= 0.0
CB-CA-HA 48.180 119.880 same as ca-ca-ha, penalty score= 0.0
CA-CA-CB 66.620 120.020 same as ca-ca-ca, penalty score= 0.0
CA-CB-CB 66.620 120.020 same as ca-ca-ca, penalty score= 0.0
CB-CB-S 61.600 120.060 same as ca-ca-ss, penalty score= 0.0
CA-CA-HA 48.180 119.880 same as ca-ca-ha, penalty score= 0.0
CA-CA-CA 66.620 120.020 same as ca-ca-ca, penalty score= 0.0
CA-CB-S 61.600 120.060 same as ca-ca-ss, penalty score= 0.0
DIHE
N -C -N -OH 4 10.000 180.000 2.000 same as X -c -n
-X , penalty score= 0.0
N -C -N -CT 4 10.000 180.000 2.000 same as X -c -n
-X , penalty score= 0.0
O -C -N -H 1 2.500 180.000 -2.000 same as hn-n -c
-o
O -C -N -H 1 2.000 0.000 1.000 same as hn-n -c
-o , penalty score= 0.0
N -C -N -H 4 10.000 180.000 2.000 same as X -c -n
-X , penalty score= 0.0
C -N -OH-HO 2 3.000 0.000 2.000 same as X -n
-oh-X , penalty score= 0.0
CT-CT-N -C 1 0.500 180.000 -4.000 same as c3-c3-n
-c
CT-CT-N -C 1 0.150 180.000 -3.000 same as c3-c3-n
-c
CT-CT-N -C 1 0.000 0.000 -2.000 same as c3-c3-n
-c
CT-CT-N -C 1 0.530 0.000 1.000 same as c3-c3-n
-c , penalty score= 0.0
H1-CT-N -C 6 0.000 0.000 2.000 same as X -c3-n
-X , penalty score= 0.0
CA-CT-N -C 6 0.000 0.000 2.000 same as X -c3-n
-X , penalty score= 0.0
O -C -N -OH 4 10.000 180.000 2.000 same as X -c -n
-X , penalty score= 0.0
O -C -N -CT 4 10.000 180.000 2.000 same as X -c -n
-X , penalty score= 0.0
HC-CT-CT-N 9 1.400 0.000 3.000 same as X
-c3-c3-X , penalty score= 0.0
C*-CA-CT-N 6 0.000 0.000 2.000 same as X
-c3-ca-X , penalty score= 0.0
S -CA-CT-N 6 0.000 0.000 2.000 same as X
-c3-ca-X , penalty score= 0.0
CT-CT-N -OH 6 0.000 0.000 2.000 same as X -c3-n
-X , penalty score= 0.0
H1-CT-N -OH 6 0.000 0.000 2.000 same as X -c3-n
-X , penalty score= 0.0
CA-CT-N -OH 6 0.000 0.000 2.000 same as X -c3-n
-X , penalty score= 0.0
CT-N -OH-HO 2 3.000 0.000 2.000 same as X -n
-oh-X , penalty score= 0.0
HA-C*-CA-CT 4 2.800 180.000 2.000 same as X
-c2-ca-X , penalty score=232.0
CB-C*-CA-CT 4 2.800 180.000 2.000 same as X
-c2-ca-X , penalty score=232.0
CT-CA-S -CB 2 0.800 180.000 2.000 same as X
-ca-ss-X , penalty score= 0.0
C*-CA-CT-CT 6 0.000 0.000 2.000 same as X
-c3-ca-X , penalty score= 0.0
S -CA-CT-CT 6 0.000 0.000 2.000 same as X
-c3-ca-X , penalty score= 0.0
H1-CT-CT-HC 9 1.400 0.000 3.000 same as X
-c3-c3-X , penalty score= 0.0
CA-CT-CT-HC 9 1.400 0.000 3.000 same as X
-c3-c3-X , penalty score= 0.0
C*-CA-CT-H1 6 0.000 0.000 2.000 same as X
-c3-ca-X , penalty score= 0.0
S -CA-CT-H1 6 0.000 0.000 2.000 same as X
-c3-ca-X , penalty score= 0.0
CA-C*-CB-CA 4 2.800 180.000 2.000 same as X
-c2-ca-X , penalty score=232.0
CA-C*-CB-CB 4 2.800 180.000 2.000 same as X
-c2-ca-X , penalty score=232.0
CB-CB-S -CA 2 0.800 180.000 2.000 same as X
-ca-ss-X , penalty score= 0.0
CA-CB-S -CA 2 0.800 180.000 2.000 same as X
-ca-ss-X , penalty score= 0.0
C*-CA-S -CB 2 0.800 180.000 2.000 same as X
-ca-ss-X , penalty score= 0.0
HA-CA-CB-C* 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
CA-CA-CB-C* 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
C*-CB-CB-CA 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
C*-CB-CB-S 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
HA-C*-CA-S 4 2.800 180.000 2.000 same as X
-c2-ca-X , penalty score=232.0
HA-C*-CB-CA 4 2.800 180.000 2.000 same as X
-c2-ca-X , penalty score=232.0
HA-C*-CB-CB 4 2.800 180.000 2.000 same as X
-c2-ca-X , penalty score=232.0
CB-C*-CA-S 4 2.800 180.000 2.000 same as X
-c2-ca-X , penalty score=232.0
CB-CA-CA-HA 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
CA-CA-CA-CB 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
CA-CA-CB-CB 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
HA-CA-CB-CB 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
CA-CB-CB-CA 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
CA-CB-CB-S 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
CA-CA-CA-HA 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
CA-CA-CA-CA 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
HA-CA-CA-HA 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
CA-CA-CB-S 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
HA-CA-CB-S 4 14.500 180.000 2.000 same as X
-ca-ca-X , penalty score= 0.0
IMPROPER
N -N -C -O 10.5 180.0 2.0 Same as X -X -c
-o , penalty score= 6.0 (use general term))
C -CT-N -OH 1.1 180.0 2.0 Using the
default value
C*-CT-CA-S 1.1 180.0 2.0 Using the
default value
CA-CB-C*-HA 1.1 180.0 2.0 Same as X -X
-ca-ha, penalty score= 38.9 (use general term))
C*-CA-CB-CB 1.1 180.0 2.0 Using the
default value
CA-CB-CA-HA 1.1 180.0 2.0 Same as X -X
-ca-ha, penalty score= 6.0 (use general term))
CA-CA-CA-HA 1.1 180.0 2.0 Same as X -X
-ca-ha, penalty score= 6.0 (use general term))
CA-CB-CB-S 1.1 180.0 2.0 Using the
default value
NONBON
N 1.8240 0.1700 same as n
H 0.6000 0.0157 same as hn
C 1.9080 0.0860 same as c
O 1.6612 0.2100 same as o
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 1.3870 0.0157 same as h1
CA 1.9080 0.0860 same as ca
C* 1.9080 0.0860 same as cc
HA 1.4590 0.0150 same as ha
CB 1.9080 0.0860 same as ca
S 2.0000 0.2500 same as ss
======
Can someone please help me in this regard...?
--
Regards,
Prasanth.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 22 2019 - 09:30:02 PDT
