[gmx-users] Cyclic Peptide Construction using pdb2gmx issue
sarah.mccartan at ucdconnect.ie
Thu Jan 26 18:42:31 CET 2017
I am having an issue building CsA cyclic peptide. It is an 11 residue
peptide with 90 atoms.
I am using the GROMOS 43a2 ff with SPC water model.
I have updated the specbond.dat file with the following:
ALA C 1 DAL N 1 0.133 ALA DAL
I have ensured it is 1 chain in the pdb file and gromacs is identifying the
bond between ALA and DAL but I still get the dangling bond error when I
select NONE for both my termini.
Do I need to modify any other files or amend any inputs?
See screen below for output from pdb2gmx:
gmx pdb2gmx -f csa_start.pdb -o csa_proc.gro -p topol.top -water spce
-missing -ter -ff gromos43a2
Force field 'gromos43a2' occurs in 2 places. pdb2gmx is using the one in the
current directory. Use interactive selection (not the -ff option) if
you would prefer a different one.
Using the Gromos43a2 force field in directory ./gromos43a2.ff
Opening force field file ./gromos43a2.ff/aminoacids.r2b
Read 90 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 11 residues with 90 atoms
chain #res #atoms
1 'X' 11 90
All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file ./gromos43a2.ff/atomtypes.atp
Reading residue database... (gromos43a2)
Opening force field file ./gromos43a2.ff/aminoacids.rtp
Sorting it all out...
Opening force field file ./gromos43a2.ff/aminoacids.hdb
Opening force field file ./gromos43a2.ff/aminoacids.n.tdb
Opening force field file ./gromos43a2.ff/aminoacids.c.tdb
Processing chain 1 'X' (90 atoms, 11 residues)
Identified residue DAL1 as a starting terminus.
Identified residue ALA11 as a ending terminus.
10 out of 10 lines of specbond.dat converted successfully
Special Atom Distance matrix:
ALA11 C89 0.133
Linking DAL-1 N-1 and ALA-11 C-89...
Select start terminus type for DAL-1
Start terminus DAL-1: None
Select end terminus type for ALA-11
End terminus ALA-11: None
Program gmx pdb2gmx, VERSION 5.1.2
Source code file:
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.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
If you need any other information please let me know.
Thanks in advance for your help,
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