Dear All,
I continued the analyze of gaff; using the latest version available in
ambertools25...
See the results below...
Best Francois
CHECK THE '/usr/local/ambertools25_src/dat/leap/parm/gaff2.dat' FILE
Identified force field in 'frcmod.user': GAFF version 2.2.20 - 2021
No_reversed_bond_FF_parameter found
Total_bond_lines processed: 1335
Unique_bond_FF_parameters detected: 1335
No_reversed_angle_FF_parameter found
Total_angle_lines processed: 9712
Unique_angle_FF_parameters detected: 9712
Duplicated_dihedral_angle_FF_parameter 'c3-c3-n-c_Vn=1' found 2 times
Duplicated_dihedral_angle_FF_parameter 'c3-c3-n-c_Vn=3' found 2 times
Duplicated_dihedral_angle_FF_parameter 'c3-c3-n-c_Vn=4' found 2 times
No_reversed_dihedral_angle_FF_parameter found
Total_dihedral_angle_lines processed: 1817
Unique_dihedral_angle_FF_parameters detected: 1814
Reversed_improper_dihedral_angle_FF_parameter found: c2-c-c2-c3
<--> c-c2-c2-c3
Reversed_improper_dihedral_angle_FF_parameter found: ca-c-ca-c3
<--> c-ca-ca-c3
Reversed_improper_dihedral_angle_FF_parameter found: n2-ca-ca-n2
<--> ca-n2-ca-n2
Reversed_improper_dihedral_angle_FF_parameter found: n2-ca-ca-n2
<--> ca-n2-ca-n2
Total_improper_dihedral_angle_lines processed: 38
Unique_improper_dihedral_angle_FF_parameters detected: 38
laptop:~/Work/PyRED/> grep -n "c3-c3-n -c"
/usr/local/ambertools25_src/dat/leap/parm/gaff2.dat
12147:c3-c3-n -c 1 0.650 180.000 -4.000
sialic2 GA AUE=1.1541 RMSE=1.2847 TorTyp
12148:c3-c3-n -c 1 0.030 180.000 -3.000
sialic2 GA AUE=1.1541 RMSE=1.2847 TorTyp
12149:c3-c3-n -c 1 2.260 0.000 1.000
sialic2 GA AUE=1.1541 RMSE=1.2847 TorTyp
12150:c3-c3-n -c 1 0.100 180.000 -4.000 p19
GA AUE=0.2882 RMSE=0.4031 TorType=2
12151:c3-c3-n -c 1 0.170 0.000 -3.000 p19
GA AUE=0.2882 RMSE=0.4031 TorType=2
12152:c3-c3-n -c 1 1.020 180.000 1.000 p19
GA AUE=0.2882 RMSE=0.4031 TorType=2
-> At least the lines are consecutive so more easy to be differentiated...
GAFF '/usr/local/ambertools25_src/dat/leap/parm/gaff2.dat' -
identify the atom types:
Total at.types: 99 - identified (hopefully) at.types: 97 -
unidentified/useless at.types: 2
C at.types: 21 - H at.types: 13 - N at.types: 34 - O at.types: 6 - P
at.types: 11 - S at.types: 10 - X at.types: 4
GAFF - check the generic dihedral angle FF paremeters (such as X -c3-c3-X):
X c p5 X - frcmod_path = 4 -- calc_path = 6 -- error
X c py X - frcmod_path = 4 -- calc_path = 6 -- error
X c1 nb X - frcmod_path = 2 -- calc_path = 1 -- error
X c1 nc X - frcmod_path = 2 -- calc_path = 1 -- error
X c1 nd X - frcmod_path = 2 -- calc_path = 1 -- error
X c1 ne X - frcmod_path = 2 -- calc_path = 1 -- error
X c1 nf X - frcmod_path = 2 -- calc_path = 1 -- error
X c3 n2 X - frcmod_path = 6 -- calc_path = 3 -- error
X c3 ne X - frcmod_path = 6 -- calc_path = 3 -- error
X c3 nf X - frcmod_path = 6 -- calc_path = 3 -- error
X ca n4 X - frcmod_path = 4 -- calc_path = 6 -- error
X n n4 X - frcmod_path = 4 -- calc_path = 6 -- error
X n1 nb X - frcmod_path = 2 -- calc_path = 1 -- error
X n1 nc X - frcmod_path = 2 -- calc_path = 1 -- error
X n1 nd X - frcmod_path = 2 -- calc_path = 1 -- error
X n1 ne X - frcmod_path = 2 -- calc_path = 1 -- error
X n1 nf X - frcmod_path = 2 -- calc_path = 1 -- error
X ne px X - frcmod_path = 3 -- calc_path = 2 -- error
X nf px X - frcmod_path = 3 -- calc_path = 2 -- error
X n3 oh X - frcmod_path = 1 -- calc_path = 2 -- error
X n3 os X - frcmod_path = 1 -- calc_path = 2 -- error
X n3 sh X - frcmod_path = 1 -- calc_path = 2 -- error
X n3 ss X - frcmod_path = 1 -- calc_path = 2 -- error
X n4 p4 X - frcmod_path = 4 -- calc_path = 6 -- error
X n4 px X - frcmod_path = 4 -- calc_path = 6 -- error
X na p2 X - frcmod_path = 1 -- calc_path = 2 -- error
X na pe X - frcmod_path = 1 -- calc_path = 2 -- error
X na pf X - frcmod_path = 1 -- calc_path = 2 -- error
X no p2 X - frcmod_path = 1 -- calc_path = 2 -- error
X no pe X - frcmod_path = 1 -- calc_path = 2 -- error
X no pf X - frcmod_path = 1 -- calc_path = 2 -- error
607 generic dihedral angles found...
Similar 'results' with all the gaff files...
For instance:
laptop:~/Work/PyRED/> grep -nE "X -ca-n4-X |X -c2-n4-X "
/usr/local/ambertools25_src/dat/leap/parm/gaff2.dat
11267:X -c2-n4-X 6 0.000 180.000 3.000 intrpol.
11356:X -ca-n4-X 4 7.000 0.000 2.000
Dividing a potential by 6 or 4 does not matter if it is = 0, but this
is different with a potential = 7 for instance
laptop:~/Work/PyRED/> bc -l
bc 1.07.1
Copyright 1991-1994, 1997, 1998, 2000, 2004, 2006, 2008, 2012-2017
Free Software Foundation, Inc.
This is free software with ABSOLUTELY NO WARRANTY.
For details type `warranty'.
7/4
1.75000000000000000000
7/6
1.16666666666666666666
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 Wed Oct 01 2025 - 01:00:02 PDT
