[gmx-users] struggles with cyclic peptides

[Nikhil]

Thanks Mark for your reply,
can you tell me the mechanism of terminal selection in gromacs or any 
source of information regarding that?
When i select None as per the mail archive information it gives an error 
here im pasting the pdb2gmx out put 

Using the Charmm27 force field in directory charmm27.ff

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: TIP5P   TIP 5-point (see http://redmine.gromacs.org/issues/1348 for 
issues)
 5: SPC     simple point charge
 6: SPC/E   extended simple point charge
 7: 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 cpn.pdb...
WARNING: all CONECT records are ignored
Read 67 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 4 chains and 0 blocks of water and 4 residues with 67 atoms

  chain  #res #atoms
  1 'A'     1     10  
  2 'B'     1     19  
  3 'C'     1     17  
  4 'D'     1     21  

All occupancies are one
Opening force field file 
/usr/share/gromacs/top/charmm27.ff/atomtypes.atp
Atomtype 213
Reading residue database... (charmm27)
Opening force field file 
/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp
Residue 44
Sorting it all out...
Opening force field file /usr/share/gromacs/top/charmm27.ff/dna.rtp
Residue 48
Sorting it all out...
Opening force field file /usr/share/gromacs/top/charmm27.ff/lipids.rtp
Residue 60
Sorting it all out...
Opening force field file /usr/share/gromacs/top/charmm27.ff/rna.rtp
Residue 64
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
Processing chain 1 'A' (10 atoms, 1 residues)
Identified residue ALA1 as a starting terminus.
Identified residue ALA1 as a ending terminus.
9 out of 9 lines of specbond.dat converted successfully
Select start terminus type for ALA-1
 0: NH3+
 1: NH2
 2: None
2
Start terminus ALA-1: None
Select end terminus type for ALA-1
 0: COO-
 1: COOH
 2: CT2
 3: CT3
 4: None
4
End terminus ALA-1: None

-------------------------------------------------------
Program pdb2gmx, VERSION 5.0.2
Source code file: /build/buildd/gromacs-
5.0.2/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091

Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your 
coordinate file, add a new terminal database entry (.tdb), or select the 
proper existing terminal entry.



the command i gave was pdb2gmx -f cpn.pdb -ter 

when i select there is additional hydrogen and oxygen present .
Thanks for the time

(i thought if i reply to  mail it will come under the thread,sorry for 
that,i hope this is the way to comment/replay under one thread )