[gmx-users] amber to gromacs error
Yun Shi
yunshi09 at gmail.com
Sun Dec 9 19:07:28 CET 2012
On Sun, Dec 9, 2012 at 9:46 AM, Albert <mailmd2011 at gmail.com> wrote:
> 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)
>
>
Not sure about "too few ...". But it seems you have some atoms with
type "3C" that is not included (defined) in top files.
> 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:
>
My resulting .top and .gro files worked well without these "include
..." stuff, and I believe all the atom types and vdw parameters, bond,
angle, and dihedral parameters, as well as atomic charges have already
been included in the resulting .top file.
> ; 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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Yun
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