Dear All,
I ran a script to check gaff2:
It looks like there are duplicate/different values for several
dihedral angles/improper angles.
(see below; 'frcmod.user' is 'gaff211.dat' from AmberTools24).
Did I miss something?
Best Francois
laptop:~/Work/P9709/> bash Check-parm.sh ./frcmod.user
No reverse bond found
Total bond lines processed: 935
Unique bonds detected: 935
No reverse angle found
Total angle lines processed: 5312
Unique angles detected: 5312
Reverse dihedral found: c3-c3-c3-hc_per=3 <--> hc-c3-c3-c3_per=3
Reverse dihedral found: c3-c3-n-c_per=-4 <--> c-n-c3-c3_per=-4
Reverse dihedral found: c3-c3-n-c_per=-3 <--> c-n-c3-c3_per=-3
Reverse dihedral found: c3-c3-n-c_per=1 <--> c-n-c3-c3_per=1
Reverse dihedral found: ca-ca-ce-c2_per=2 <--> c2-ce-ca-ca_per=2
Reverse dihedral found: c3-c3-os-c3_per=-3 <--> c3-os-c3-c3_per=-3
Total dihedral angle lines processed: 1128
Unique dihedral angles detected: 1128
Reordered improper found 5: c2-c-c2-c3 <--> c-c2-c2-c3
Reordered improper found 5: ca-c-ca-c3 <--> c-ca-ca-c3
Reordered improper found 1: n2-ca-ca-n2 <--> ca-n2-ca-n2
Reordered improper found 5: n2-ca-ca-n2 <--> ca-n2-ca-n2
Total improper angle lines processed: 38
Unique improper angles detected: 38
laptop:~/PyRED-P9709/> grep -En "c3-c3-c3-hc|hc-c3-c3-c3"
/usr/local/amber24/dat/leap/parm/gaff211.dat
7052:hc-c3-c3-c3 1 0.080 0.000 3 m2 SS
AUE=0.2468 RMSE=0.2989 TorType=2
7118:c3-c3-c3-hc 1 0.080 0.000 3 t2 SS
AUE=0.2507 RMSE=0.3027 TorType=3
laptop:~/PyRED-P9709/> grep -En "c3-c3-n -c|c -n -c3-c3"
/usr/local/amber24/dat/leap/parm/gaff211.dat
7041:c -n -c3-c3 1 0.100 180.000 -4 p19
GA AUE=0.2882 RMSE=0.4031 TorType=2
7042:c -n -c3-c3 1 0.170 0.000 -3 p19
GA AUE=0.2882 RMSE=0.4031 TorType=2
7043:c -n -c3-c3 1 1.020 180.000 1 p19
GA AUE=0.2882 RMSE=0.4031 TorType=2
7120:c3-c3-n -c 1 0.650 180.000 -4
sialic2 GA AUE=1.1541 RMSE=1.2847 TorType=3
7121:c3-c3-n -c 1 0.030 180.000 -3
sialic2 GA AUE=1.1541 RMSE=1.2847 TorType=3
7122:c3-c3-n -c 1 2.260 0.000 1
sialic2 GA AUE=1.1541 RMSE=1.2847 TorType=3
laptop:~/PyRED-P9709/> grep -En "ca-ca-ce-c2|c2-ce-ca-ca"
/usr/local/amber24/dat/leap/parm/gaff211.dat
7089:c2-ce-ca-ca 1 0.505 180.000 2 add6f
SS AUE=0.2273 RMSE=0.3302 TorType=3
7249:ca-ca-ce-c2 1 0.618 180.000 2 c24
SS AUE=0.2364 RMSE=0.3330 TorType=3
laptop:~/PyRED-P9709/> grep -En "c3-c3-os-c3|c3-os-c3-c3"
/usr/local/amber24/dat/leap/parm/gaff211.dat
7032:c3-os-c3-c3 1 0.240 0.000 -3 p29
GA AUE=0.4256 RMSE=0.5201 TorType=2
7033:c3-os-c3-c3 1 0.160 0.000 2 p29
GA AUE=0.4256 RMSE=0.5201 TorType=2
7412:c3-c3-os-c3 1 0.910 0.000 -3
lactose1,ccoc GA AUE=1.5236 RMSE=2.4206 TorType=3
7413:c3-c3-os-c3 1 1.000 0.000 -2
7414:c3-c3-os-c3 1 0.000 0.000 1
laptop:~/PyRED-P9709/>
laptop:~/PyRED-P9709/> grep -En "c2-c -c2-c3|c -c2-c2-c3" gaff211.dat
7488:c -c2-c2-c3 1.1 180. 2. dac
guess, 9/94
7493:c2-c -c2-c3 1.1 180. 2.
laptop:~/PyRED-P9709/> grep -En "ca-c -ca-c3|c -ca-ca-c3" gaff211.dat
7489:c -ca-ca-c3 1.1 180. 2. dac
guess, 9/94
7510:ca-c -ca-c3 1.1 180. 2.
laptop:~/PyRED-P9709/> grep -En "n2-ca-ca-n2|ca-n2-ca-n2" gaff211.dat
7512:ca-n2-ca-n2 1.1 180. 2. dac, 10/94
7516:n2-ca-ca-n2 1.1 180. 2. dac
guess, 9/94
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Received on Thu Sep 11 2025 - 00:00:02 PDT
