Thanks for mentioning my errors. I have corrected them. But now the problem is there is no rtp entry for NH2 in charmm. Here is what happens now-
Using the Charmm27 force field in directory charmm27.ff pdb2gmx -f bestins.pdb -o first.gro -ter *entering 8 for charmm 27 force field* Opening force field file /usr/share/gromacs/top/charmm27.ff/watermodels.dat Select the Water Model: 1: TIP3P TIP 3-point, recommended 2: TIP4P TIP 4-point 3: TIPS3P CHARMM TIP 3-point with LJ on H's (note: twice as slow in GROMACS) 4: SPC simple point charge 5: SPC/E extended simple point charge 6: None 1 Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.r2b Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.r2b Reading bestins.pdb... WARNING: all CONECT records are ignored Read 416 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 2 chains and 0 blocks of water and 32 residues with 416 atoms chain #res #atoms 1 'A' 23 167 2 'B' 32 249 WARNING: there were 1 atoms with zero occupancy and 15 atoms with occupancy unequal to one (out of 416 atoms). Check your pdb file. Opening force field file /usr/share/gromacs/top/charmm27.ff/atomtypes.atp Atomtype 1 Reading residue database... (charmm27) Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.rtp Residue 43 Sorting it all out... Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.rtp Residue 47 Sorting it all out... Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.rtp Residue 59 Sorting it all out... Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.rtp Residue 63 Sorting it all out... Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.hdb Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.hdb Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.hdb Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.n.tdb Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.n.tdb Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.c.tdb Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.c.tdb Back Off! I just backed up topol.top to ./#topol.top.17# Processing chain 1 'A' (167 atoms, 23 residues) There are 31 donors and 35 acceptors There are 38 hydrogen bonds Identified residue ACE1 as a starting terminus. Identified residue NH223 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS7 CYS8 CYS12 SG46 SG52 SG79 CYS8 SG52 0.691 CYS12 SG79 0.203 0.820 CYS21 SG157 1.140 1.613 1.215 Linking CYS-7 SG-46 and CYS-12 SG-79... Select start terminus type for ACE-1 0: NH3+ 1: NH2 2: None 2 Start terminus ACE-1: None ------------------------------------------------------- Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/resall.c, line: 581 Fatal error: Residue 'NH2' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors
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