... there is also:
[...]
Reverse dihedral found: c3-c3-c-o_per=(-)2 <--> o-c-c3-c3_per=(-)2
[...]
laptop:~/Work/P9709/> grep -En "c3-c3-c -o|o -c -c3-c3"
/usr/local/amber24/dat/leap/parm/gaff211.dat
7360:o -c -c3-c3 1 0.270 180.000 2 p14
SS AUE=0.2361 RMSE=0.3321 TorType=3
7409:c3-c3-c -o 1 0.030 180.000 -2
sialic1,t37,t41 GA AUE=0.7374 RMSE=0.9897 TorType=3
7410:c3-c3-c -o 1 0.550 180.000 -3
7411:c3-c3-c -o 1 0.740 0.000 1
Best Francois
Quoting FyD via AMBER <amber.ambermd.org>:
> 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 - 00:30:03 PDT
