I used g_sas in GROMACS to analyse SASA for a .xtc file, but for another purpose of analysis, I wan to use g_sas for a .pdb file.
Has anyone used g_sas for a .pdb file?
If possible, could you please suggest another method to analyse SASA for a .pdb file?
G_sas -h says, that it should be possible to use pdb file format as well. Try something like:
g_sas -f your.pdb -s your.pdb
I've tried just now and g_sas definitely processes pdb files. What error does it give to you? Where is the pdb file from?
Which group that you choose: "Select a group for calculation of surface and a group for output"?
I got the problem: "If there are molecules in the input trajectory file
that are broken across periodic boundaries, they
cannot be made whole (or treated as whole) without
you providing a run input file."
To get a relevant answer you should provide as much information as you can...
Where is the pdb file from? Are there any broken periodic molecules? Is it single-geometry or a trajectory?
You should choose the group of atoms, the SASA of which you want to calculate.
I assume you processed the trajectory and the final pdb file contains unbroken molecule. Then it should be quite straightforward to run g_sas.
What happens when you run g_sas -f file.pdb -s file.pdb?
Select "System" both times g_sas asks.
Probably too late, but you could try a tool I wrote: https://github.com/mittinatten/freesasa, that calculates SASA from PDB-files.
I recommend VMD software for trajectory analysis
you can use "source SASA_cal_command.txt" in vmd tk consol
---------------------------------------
sasa.txt
>>
set outfile [open SASA.txt w]
set nf [molinfo top get numframes]
set protein [atomselect top "protein"]
set phob [atomselect top "hydrophobic"]
set phil [atomselect top "not hydrophobic"]
for {set i 0} {$i
Hi Maryam Olagunju How would you define "hydrophobic interactions"?
From molecular mechanics point of view, a hydrophobic interaction is not clear to define. One approach would be to simply check the contacts between ligand and the amino acids considered as hydrophobic (Leu, Ile, Phe, ...). You can do that with the "measure contacts" command. You can use my ContactFreq.tcl script
also PIC server also may be helpful
https://dx.doi.org/10.1093%2Fnar%2Fgkm423
http://pic.mbu.iisc.ernet.in/
- Badges
- Science topic