[gmx-users] contacts

[Yasser Almeida Hernández]

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.hernandez at chemie.uni-hamburg.de
office: Grindelallee 117, room 250c