hey, i am here with two basic questions:
I want to perform some analysis on monomers of pentameric protein. There is HSD residue in my protein but when i am performing hydrophobicity related analysis on it, i am getting error for the particular protonation state : like there is no hydrophobicity entry for HSD. is it possible to rename HSD residue to HIS in .XTC and .tpr files?
my second query is i have to select monomer and lets say run g_rmsf on it. How can i rewrite a trajectory with specific atom residues (monomer only) here? I didnt add chain identifiers to pdb before simulation ( A B C D).
First question:
You cannot rename a residue in the trajectory as the topology is saved in the topology file your provided to the gmx tool, e.g. the .pdb file or the .top file. You just need to put these topology file in the commend line to let the gmx tool to read it.
Second one:
As the first answer writes, you can make an index file and use thr trjconv tool of gmx to extract the specific trajectory for the selected residues. The make_ndx command and trjconv command in gmx could do this.
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