On Sun, Dec 9, 2012 at 9:46 AM, Albert <mailmd2...@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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Yun -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists