Hello,
I did a CGMD run of a membrane protein embedded in a model bilayer and I
want to compute the contacts between my protein and the PO4 beads of
certain lipid. I am using the following command:
gmx mindist -s md_protein_membrane_1.tpr -f
md_protein_membrane_centered_run1.xtc -or mindistres_1.xvg -od
mindist_1.xvg -o atm-pair_1.out -on numcont_1.xvg -tu ns -d 0.6 -n index.ndx
Then, I got the output in the numcont.xvg and atm-pair.out:
<numcont.xvg>
9.000000e+03 6
9.000011e+03 5
9.000021e+03 6
9.000030e+03 3
9.000040e+03 6
9.000051e+03 3
9.000061e+03 1
9.000070e+03 1
9.000080e+03 1
9.000091e+03 2
9.000101e+03 2
9.000110e+03 1
...
<atm-pair.out>
9.000000e+03 285 5019
9.000011e+03 286 5019
9.000021e+03 284 5019
9.000030e+03 293 5019
9.000040e+03 293 5019
9.000051e+03 299 5151
9.000061e+03 299 5151
9.000070e+03 293 5019
9.000080e+03 293 5019
9.000091e+03 293 5019
9.000101e+03 293 5019
9.000110e+03 299 5151
...
If I interpret correctly (please correct me if I am wrong), numcont.xvg
informs that -for example- at time 9.000000e+03 there are 6 contacts,
but then in atm-pair.out at that time there are 1 contact between
atom/bead 285 and 5019. Do I am missing something?
At the end what I want is to get per-residue contacts between the
protein and the PO4 beads, to map them on the protein to see which
region have more contacts.
Thanks in advance.
Yasser
--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c
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