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Protein - membrane lipids contacts
- almeida
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5 years 4 months 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
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
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- riccardo
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5 years 3 months ago - 5 years 3 months 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: 5 years 3 months ago by riccardo.
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- almeida
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5 years 3 months 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
It is any way to get all pairs for each time?
Best
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- riccardo
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5 years 3 months 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.
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- almeida
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5 years 3 months ago #7983
by almeida
Replied by almeida on topic Protein - membrane lipids contacts
Thanks!! I am using gmx select, I am getting closer ;)
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- Luciferase
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3 years 5 months ago #8769
by Luciferase
Replied by Luciferase on topic Protein - membrane lipids contacts
Hello!
I am trying pretty much the same, to get the contacts between two proteins during a Martini CG simulation to see which region has the most contacts.
You proposed to use gmx select to get to the contacts for every pair of residues at each time. Could you tell how to do that with an example maybe?
I can't find to understand it through the gromacs help pages.
Best regards
Peter
I am trying pretty much the same, to get the contacts between two proteins during a Martini CG simulation to see which region has the most contacts.
You proposed to use gmx select to get to the contacts for every pair of residues at each time. Could you tell how to do that with an example maybe?
I can't find to understand it through the gromacs help pages.
Best regards
Peter
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