[gmx-users] Re : Capping error in pdb2gmx

[siddhant jain]

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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