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-<div><br></div><div><div>Using the Charmm27 force field in directory charmm27.ff</div>
<div><div><br></div><div>pdb2gmx -f bestins.pdb -o first.gro -ter</div></div><div><br></div><div>*entering 8 for charmm 27 force field*</div><div><br></div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/watermodels.dat</div>
<div><br></div><div>Select the Water Model:</div><div> 1: TIP3P TIP 3-point, recommended</div><div> 2: TIP4P TIP 4-point</div><div> 3: TIPS3P CHARMM TIP 3-point with LJ on H's (note: twice as slow in GROMACS)</div>
<div> 4: SPC simple point charge</div><div> 5: SPC/E extended simple point charge</div><div> 6: None</div><div>1</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.r2b</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.r2b</div>
<div>Reading bestins.pdb...</div><div>WARNING: all CONECT records are ignored</div><div>Read 416 atoms</div><div>Analyzing pdb file</div><div>Splitting PDB chains based on TER records or changing chain id.</div><div>There are 2 chains and 0 blocks of water and 32 residues with 416 atoms</div>
<div><br></div><div> chain #res #atoms</div><div> 1 'A' 23 167 </div><div> 2 'B' 32 249 </div><div><br></div><div><br></div><div>WARNING: there were 1 atoms with zero occupancy and 15 atoms with</div>
<div> occupancy unequal to one (out of 416 atoms). Check your pdb file.</div><div><br></div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/atomtypes.atp</div><div>Atomtype 1</div><div>Reading residue database... (charmm27)</div>
<div>Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.rtp</div><div>Residue 43</div><div>Sorting it all out...</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.rtp</div><div>
Residue 47</div><div>Sorting it all out...</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.rtp</div><div>Residue 59</div><div>Sorting it all out...</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.rtp</div>
<div>Residue 63</div><div>Sorting it all out...</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.hdb</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.hdb</div><div>
Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.hdb</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.hdb</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb</div>
<div>Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.n.tdb</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.n.tdb</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb</div>
<div>Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.c.tdb</div><div>Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.c.tdb</div><div><br></div><div>Back Off! I just backed up topol.top to ./#topol.top.17#</div>
<div>Processing chain 1 'A' (167 atoms, 23 residues)</div><div>There are 31 donors and 35 acceptors</div><div>There are 38 hydrogen bonds</div><div>Identified residue ACE1 as a starting terminus.</div><div>Identified residue NH223 as a ending terminus.</div>
<div>8 out of 8 lines of specbond.dat converted successfully</div><div>Special Atom Distance matrix:</div><div> CYS7 CYS8 CYS12</div><div> SG46 SG52 SG79</div><div> CYS8 SG52 0.691</div>
<div> CYS12 SG79 0.203 0.820</div><div> CYS21 SG157 1.140 1.613 1.215</div><div>Linking CYS-7 SG-46 and CYS-12 SG-79...</div><div>Select start terminus type for ACE-1</div><div> 0: NH3+</div><div> 1: NH2</div>
<div> 2: None</div><div>2</div><div>Start terminus ACE-1: None</div><div><br></div><div>-------------------------------------------------------</div><div>Program pdb2gmx, VERSION 4.5.4</div><div>Source code file: /build/buildd/gromacs-4.5.4/src/kernel/resall.c, line: 581</div>
<div><br></div><div>Fatal error:</div><div>Residue 'NH2' not found in residue topology database</div><div>For more information and tips for troubleshooting, please check the GROMACS</div><div>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></div>
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