normal Protein - membrane lipids contacts

  • almeida
  • almeida's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
5 months 4 days ago #7978 by almeida
Protein - membrane lipids contacts was created by almeida
Hi all,

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 LIPIDS_index.ndx

In the outputs numcont.xvg and atm-pair.out I got (fragment):

<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

Please Log in or Create an account to join the conversation.

More
4 months 2 weeks ago - 4 months 2 weeks ago #7980 by riccardo
Replied by riccardo on topic Protein - membrane lipids contacts
What you wrote is correct; I just want to point out that the pair of particles listed in the atm-pair.out is the pair of atoms which is *the closest* at that particular time. For example, at time 9.000051e+03 there are 3 contacts, i.e., 3 distances are shorter than the cutoff of 0.6 nm, and the shortest of these distances is between particles 299 and 5151.
Last edit: 4 months 2 weeks ago by riccardo.

Please Log in or Create an account to join the conversation.

  • almeida
  • almeida's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
4 months 2 weeks ago #7981 by almeida
Replied by almeida on topic Protein - membrane lipids contacts
Thank you very much for the reply!

It is any way to get all pairs for each time?

Best

Please Log in or Create an account to join the conversation.

More
4 months 2 weeks ago #7982 by riccardo
Replied by riccardo on topic Protein - membrane lipids contacts
I think that with gmx mindist you cannot. However, gmx select with the option "-oi" (plus perhaps "-resnr") may get you there. I haven't really used it myself though, so perhaps you can try to experiment a bit with it and post back here in case of problems.

Please Log in or Create an account to join the conversation.

  • almeida
  • almeida's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
4 months 2 weeks ago #7983 by almeida
Replied by almeida on topic Protein - membrane lipids contacts
Thanks!! I am using gmx select, I am getting closer ;)

Please Log in or Create an account to join the conversation.

Time to create page: 0.085 seconds