>If you want further help, you will need to paste your .rtp entry(s), the >N-terminal fragment of your pdb2gmx -f input, pdb2gmx command line, full >pdb2gmx output, the N-terminal fragment of the grompp -c input, grompp >>command line, and full grompp output. You may think your context is clear, >but nobody else is paying your problem as much attention as you are. I won't >help further if you only provide partial information.
1. rtp entry [ FVAL ] [ atoms ] CN C 0.357 0 ON O -0.51 1 H1 HA 0.100 2 N NH1 -0.423 3 HN H 0.333 4 CA CT1 0.034 5 HA HB 0.09 6 CB CT1 -0.093 7 HB HA 0.09 8 CG1 CT3 -0.268 9 HG11 HA 0.09 10 HG12 HA 0.09 11 HG13 HA 0.09 12 CG2 CT3 -0.268 13 HG21 HA 0.09 14 HG22 HA 0.09 15 HG23 HA 0.09 16 C C 0.528 17 O O -0.510 18 [ bonds ] CN H1 CN ON CN N N HN CA N CA HA CA C C O CA CB CB HB CB CG1 CB CG2 CG2 HG21 CG2 HG22 CG2 HG23 CG1 HG11 CG1 HG12 CG1 HG13grompp -f ions.mdp -c monomer_solv.gro -p topol.top -o ions.tpr [ impropers ] CN N ON H1 2. hdb entry FVAL 6 1 1 H1 CN N ON 1 1 HN N C CA 1 5 HA CA N C CB 1 5 HB CB CA CG1 CG2 3 4 HG1 CG1 CB CA 3 4 HG2 CG2 CB CA 3. N-terminal fragment HETATM 1 CN FVAL 1 -0.721 1.600 1.249 HETATM 2 ON FVAL 1 -0.839 2.806 1.453 ATOM 3 N FVAL 1 -1.227 0.728 2.125 ATOM 4 CA FVAL 1 -1.918 1.159 3.323 ATOM 5 C FVAL 1 -1.969 2.678 3.410 ATOM 6 O FVAL 1 -0.931 3.335 3.447 ATOM 7 CB FVAL 1 -1.219 0.644 4.576 ATOM 8 CG1 FVAL 1 0.208 1.178 4.618 ATOM 9 CG2 FVAL 1 -1.976 1.118 5.812 4. pdb2gmx command #pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter 5. pdb2gmx output Using the Charmm36-modified force field in directory ./charmm36-modified.ff Opening force field file ./charmm36-modified.ff/aminoacids.r2b Opening force field file ./charmm36-modified.ff/rna.r2b Reading monomer.pdb... Read 177 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 24 residues with 177 atoms chain #res #atoms 1 ' ' 24 177 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./charmm36-modified.ff/atomtypes.atp Atomtype 1 Reading residue database... (charmm36-modified) Opening force field file ./charmm36-modified.ff/aminoacids.rtp Residue 42 Sorting it all out... Opening force field file ./charmm36-modified.ff/dna.rtp Residue 46 Sorting it all out... Opening force field file ./charmm36-modified.ff/lipids.rtp Residue 82 Sorting it all out... Opening force field file ./charmm36-modified.ff/rna.rtp Residue 86 Sorting it all out... Opening force field file ./charmm36-modified.ff/aminoacids.hdb Opening force field file ./charmm36-modified.ff/dna.hdb Opening force field file ./charmm36-modified.ff/lipids.hdb Opening force field file ./charmm36-modified.ff/rna.hdb Opening force field file ./charmm36-modified.ff/aminoacids.n.tdb Opening force field file ./charmm36-modified.ff/dna.n.tdb Opening force field file ./charmm36-modified.ff/rna.n.tdb Opening force field file ./charmm36-modified.ff/aminoacids.c.tdb Opening force field file ./charmm36-modified.ff/dna.c.tdb Opening force field file ./charmm36-modified.ff/rna.c.tdb Back Off! I just backed up topol.top to ./#topol.top.1# Processing chain 1 (177 atoms, 24 residues) Identified residue FVAL1 as a starting terminus. Identified residue GLY24 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for FVAL-1 0: NH3+ 1: NH2 2: None 2 Start terminus FVAL-1: None Select end terminus type for GLY-24 0: COO- 1: COOH 2: CT2 3: CT3 4: None 0 End terminus GLY-24: COO- Opening force field file ./charmm36-modified.ff/aminoacids.arn Opening force field file ./charmm36-modified.ff/dna.arn Opening force field file ./charmm36-modified.ff/rna.arn Checking for duplicate atoms.... Now there are 24 residues with 360 atoms Making bonds... Warning: Long Bond (1-18 = 0.357049 nm) Number of bonds was 361, now 361 Generating angles, dihedrals and pairs... Before cleaning: 920 pairs Before cleaning: 925 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 22 cmap torsion pairs There are 925 dihedrals, 49 impropers, 642 angles 911 pairs, 361 bonds and 0 virtual sites Total mass 2510.906 a.m.u. Total charge 1.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.1# Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: monomer.pdb. The Charmm36-modified force field and the tip3p water model are used. --------- ETON ESAELP ------------ 6. N-terminal fragment of the grompp -c input 1FVAL CN 1 3.040 1.903 2.415 1FVAL ON 2 3.028 2.024 2.435 1FVAL N 3 2.989 1.816 2.503 1FVAL HN 4 3.030 1.758 2.432 1FVAL CA 5 2.920 1.859 2.622 1FVAL HA 6 2.829 1.820 2.613 1FVAL CB 7 2.990 1.807 2.748 1FVAL HB 8 2.992 1.707 2.746 1FVAL CG1 9 3.133 1.861 2.752 1FVAL HG11 10 3.179 1.827 2.834 1FVAL HG12 11 3.182 1.830 2.671 1FVAL HG13 12 3.131 1.961 2.753 1FVAL CG2 13 2.914 1.855 2.871 1FVAL HG21 14 2.960 1.821 2.953 1FVAL HG22 15 2.912 1.955 2.873 1FVAL HG23 16 2.821 1.820 2.868 1FVAL C 17 2.915 2.011 2.631 1FVAL H1 18 2.825 2.031 2.670 1FVAL O 19 3.019 2.076 2.635 7.grompp command line # grompp -f ions.mdp -c monomer_solv.gro -p topol.top -o ions.tpr 8. grompp output Generated 21528 of the 21528 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 18355 of the 21528 1-4 parameter combinations ERROR 1 [file topol.top, line 416]: No default Bond types ERROR 2 [file topol.top, line 1693]: No default U-B types ERROR 3 [file topol.top, line 1694]: No default U-B types ERROR 4 [file topol.top, line 2338]: No default Proper Dih. types ERROR 5 [file topol.top, line 3265]: No default Improper Dih. types Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 3365]: System has non-zero total charge: 1.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. There was 1 note ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/grompp.c, line: 1372 Fatal error: There were 5 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I hope there are enough. If anything else, please let me know. Thanks, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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? 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