[gmx-users] struggles with cyclic peptides

[Justin Lemkul]

On 9/13/15 12:51 PM, Nikhil wrote:
> 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
>

Your residues need to be in the same chain, otherwise none of this will work.

-Justin

> 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 )
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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