Dear Gromacs users,
I'm trying to calculate the distance between two specific residues of the active site of my protein in MD. I have made separate .index file of two specific groups. Then I am trying this command
" gmx distance -f md_0_1.xtc -s md_0_1.tpr -oav distance.xvg -select -n index.ndx -to ns ". When I am selecting my residues numbers for option -select in the above command. an error appeared that pairs are not found in your selection residues (1st residue "11 atoms" and 2nd residue "15 atoms" ). Kindly guide me on how I calculate the distance between two specific residues in MD.
Thanks,
Dear Abid
First, make an index file and show those residues in index file. Check .gro file and write the residue index for example 15ALA (use 15) or 35GLY (use 35). Then, while calculating distance indicate index file: g_dist .... -n index.ndx and show those residues. you can get distance between two residues.
Dear Abid,
Could you please tell me how you solved this? I am facing same errors.
Hello Souvik ,
Even I was also facing the same problem from one day but today I found that I was giving the wrong selection command in index file . Suppose you want to calculate distance between two residues of their CA atom , then you give "r1|r2| & a CA " in index file group and then give the command gmx distance -f md.xtc -s md.tpr -n index.ndx -oav distance.xvg . Because each selection should consist of pairs of positions . In such types of problems normally we give wrong selection in index file and that we can rectify it by help command .
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