[gmx-users] amber to gromacs error
Albert
mailmd2011 at gmail.com
Sun Dec 9 18:46:35 CET 2012
hello:
I am using the command:
acpype.py -p prmtop -x S13.rst
to convert Amber system into Gromacs system, but it failed when I try to
generate .tpr file:
WARNING 1 [file prmtop_GMX.top, line 19]:
Too few parameters on line (source file toppush.c, line 300)
WARNING 2 [file prmtop_GMX.top, line 22]:
Too few parameters on line (source file toppush.c, line 300)
Generated 820 of the 820 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 820 of the 820 1-4 parameter combinations
-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1166
Fatal error:
Atomtype 3C not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra)
My ligand contains both glycam FF and GAFF parameters from Amber. It is
quite strange when I open the generated .top file because there is even
no "include "amber99SB.ff/forcefiled.itp" line.... Here is the .top file
I got:
; prmtop_GMX.top created by acpype (Rev: 7234) on Sun Dec 9 18:35:28 2012
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
N3 N3 0.00000 0.00000 A 3.25000e-01 7.11280e-01
; 1.82 0.1700
H H 0.00000 0.00000 A 1.06908e-01 6.56888e-02
; 0.60 0.0157
CX CX 0.00000 0.00000 A 3.39967e-01 4.57730e-01
; 1.91 0.1094
HP HP 0.00000 0.00000 A 1.95998e-01 6.56888e-02
; 1.10 0.0157
CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01
; 1.91 0.1094
HC HC 0.00000 0.00000 A 2.64953e-01 6.56888e-02
; 1.49 0.0157
C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01
; 1.91 0.0860
O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01
; 1.66 0.2100
N N 0.00000 0.00000 A 3.25000e-01 7.11280e-01
; 1.82 0.1700
H1 H1 0.00000 0.00000 A 2.47135e-01 6.56888e-02
; 1.39 0.0157
3C 3C 0.00000 0.00000 A 3.39967e-01 4.57730e-01
; 1.91 0.1094
OH OH 0.00000 0.00000 A 3.06647e-01 8.80314e-01
; 1.72 0.2104
HO HO 0.00000 0.00000 A 0.00000e+00 0.00000e+00
; 0.00 0.0000
2C 2C 0.00000 0.00000 A 3.39967e-01 4.57730e-01
; 1.91 0.1094
S S 0.00000 0.00000 A 3.56359e-01 1.04600e+00
; 2.00 0.2500
CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01
; 1.91 0.0860
HA HA 0.00000 0.00000 A 2.59964e-01 6.27600e-02
; 1.46 0.0150
CO CO 0.00000 0.00000 A 3.39967e-01 3.59824e-01
; 1.91 0.0860
O2 O2 0.00000 0.00000 A 2.95992e-01 8.78640e-01
; 1.66 0.2100
C* C* 0.00000 0.00000 A 3.39967e-01 3.59824e-01
; 1.91 0.0860
CW CW 0.00000 0.00000 A 3.39967e-01 3.59824e-01
; 1.91 0.0860
H4 H4 0.00000 0.00000 A 2.51055e-01 6.27600e-02
; 1.41 0.0150
NA NA 0.00000 0.00000 A 3.25000e-01 7.11280e-01
; 1.82 0.1700
CN CN 0.00000 0.00000 A 3.39967e-01 3.59824e-01
; 1.91 0.0860
CB CB 0.00000 0.00000 A 3.39967e-01 3.59824e-01
; 1.91 0.0860
C8 C8 0.00000 0.00000 A 3.39967e-01 4.57730e-01
; 1.91 0.1094
CC CC 0.00000 0.00000 A 3.39967e-01 3.59824e-01
; 1.91 0.0860
NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01
; 1.82 0.1700
CR CR 0.00000 0.00000 A 3.39967e-01 3.59824e-01
; 1.91 0.0860
H5 H5 0.00000 0.00000 A 2.42146e-01 6.27600e-02
; 1.36 0.0150
N2 N2 0.00000 0.00000 A 3.25000e-01 7.11280e-01
; 1.82 0.1700
CV CV 0.00000 0.00000 A 3.39967e-01 3.59824e-01
; 1.91 0.0860
SH SH 0.00000 0.00000 A 3.56359e-01 1.04600e+00
; 2.00 0.2500
HS HS 0.00000 0.00000 A 1.06908e-01 6.56888e-02
; 0.60 0.0157
Ho Ho 0.00000 0.00000 A 3.56359e-02 1.25520e-01
; 0.20 0.0300
Oh Oh 0.00000 0.00000 A 3.06647e-01 8.80314e-01
; 1.72 0.2104
Cg Cg 0.00000 0.00000 A 3.39967e-01 4.57730e-01
; 1.91 0.1094
H2 H2 0.00000 0.00000 A 2.29317e-01 6.56888e-02
; 1.29 0.0157
Os Os 0.00000 0.00000 A 3.00001e-01 7.11280e-01
; 1.68 0.1700
Na+ Na+ 0.00000 0.00000 A 2.43928e-01 3.65846e-01
; 1.37 0.0874
OW OW 0.00000 0.00000 A 3.15075e-01 6.35968e-01
; 1.77 0.1520
HW HW 0.00000 0.00000 A 0.00000e+00 0.00000e+00
; 0.00 0.0000
[ moleculetype ]
;name nrexcl
prmtop 3
[ atoms ]
; nr type resi res atom cgnr charge mass ; qtot
bond_type
1 N3 1 ALA N 1 0.141400 14.01000 ; qtot 0.141
2 H 1 ALA H1 2 0.199700 1.00800 ; qtot 0.341
3 H 1 ALA H2 3 0.199700 1.00800 ; qtot 0.541
4 H 1 ALA H3 4 0.199700 1.00800 ; qtot 0.741
.....
7925 Cg 512 LIG C1 7925 0.509001 12.01000 ; qtot -0.685
7926 H2 512 LIG H1 7926 0.000000 1.00800 ; qtot -0.685
7927 Cg 512 LIG C2 7927 0.246000 12.01000 ; qtot -0.439
7928 H1 512 LIG H2 7928 0.000000 1.00800 ; qtot -0.439
7929 Oh 512 LIG O2 7929 -0.713001 16.00000 ; qtot -1.152
7930 Ho 512 LIG H2O 7930 0.437000 1.00800 ; qtot -0.715
....
[ bonds ]
; ai aj funct r k
1 2 1 1.0100e-01 3.6317e+05 ; N - H1
1 3 1 1.0100e-01 3.6317e+05 ; N - H2
....
[ angles ]
; ai aj ak funct theta cth
1 5 6 1 1.0950e+02 4.1840e+02 ; N -
CA - HA
1 5 7 1 1.1120e+02 6.6944e+02 ; N -
CA - CB
....
[ dihedrals ] ; propers
; treated as RBs in GROMACS to use combine multiple AMBER torsions per
quartet
; i j k l func C0 C1 C2
C3 C4 C5
1 5 7 8 3 0.65084 1.95253 0.00000
-2.60338 0.00000 0.00000 ; N- CA- CB- HB1
1 5 7 9 3 0.65084 1.95253 0.00000
-2.60338 0.00000 0.00000 ; N- CA- CB- HB2
1 5 7 10 3 0.65084 1.95253 0.00000
-2.60338 0.00000 0.00000 ; N- CA- CB- HB3
....
[ moleculetype ]
; molname nrexcl
NA+ 1
[ atoms ]
; id at type res nr residu name at name cg nr charge mass
1 IP 1 NA+ NA+ 1 1 22.9898
[ moleculetype ]
; molname nrexcl ; TIP3P model
WAT 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OW 1 WAT O 1 -0.834 16.00000
2 HW 1 WAT H1 1 0.417 1.00800
3 HW 1 WAT H2 1 0.417 1.00800
#ifdef FLEXIBLE
[ bonds ]
; i j funct length force.c.
1 2 1 0.09572 462750.4 0.09572 462750.4
1 3 1 0.09572 462750.4 0.09572 462750.4
[ angles ]
; i j k funct angle force.c.
2 1 3 1 104.520 836.800 104.520 836.800
#else
[ settles ]
; i j funct length
1 1 0.09572 0.15139
[ exclusions ]
1 2 3
2 1 3
3 1 2
#endif
[ system ]
prmtop
[ molecules ]
; Compound nmols
prmtop 1
NA+ 1
WAT 16028
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