On 5/27/12 12:05 PM, vijaya subramanian wrote:
Hi
I am trying to add conect records to a cg trajectory under gromacs 4.5.4 as
follows:
trjconv -s CONECT.PDB -f traj.xtc -conect -o testconect.pdb
or with one frame
trjconv -s CONECT.PDB -f oneframe.pdb -conect -o testconect.pdb
but dont see any conect records in the output file.
The conect records are in the input to -s , conect.pdb and in the following
format:
...
ATOM 4125 CA HIS X 173 107.816 143.564 71.946 1.00 0
ATOM 4126 CA THR X 174 110.288 142.372 69.327 1.00 0
ATOM 4127 CA LEU X 175 111.958 139.227 70.607 1.00 0
ATOM 4128 CA GLY X 176 108.771 138.107 72.357 1.00 0
CONECT 1 2
CONECT 2 3
CONECT 3 4
CONECT 4 5
CONECT 5 6
CONECT 6 7
CONECT 7 8
CONECT 8 9
CONECT 9 10
CONECT 10 11
CONECT 11 12
CONECT 12 13
CONECT 13 14
CONECT 14 15
CONECT 15 16
CONECT 16 17
CONECT 17 18
CONECT 18 19
CONECT 19 20
CONECT 20 21
CONECT 21 22
...
What should I do differently to get the conect records in the output file?
Try using a .tpr file, where bonds are present according to the topology.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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