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Today's Topics:
1. Clustering energy minimized equally space frames (ashish bihani)
2. Re
I extracted [was instructed to extract] trajectory frames at every 10 ps from a
10ns xtc file and energy minimized each of them. How do I cluster them?
I tried to do ls *.gro | gmx cluster -f {.}.gro , did not work.
I concatenated the frames and made an xtc file and tried to cluster it in
PRODRG has generated force field parameters for Inositol Pyrophosphate (as
mentioned in the tutorials). I reformatted atoms, bonds, bond angles, dihedrals
and impropers by imitating the format followed in the definitions of other
residues in aminoacids.rtp. But I am not able to find a format
Hello,
I have understood my mistakes that I reported in previous queries of this
string. now, I am proceeding more systematically.
I have generated ff parameters for Inositol Pyrophosphate with the help of
PRODRG server (as mentioned in the tutorials) as a residue and added it to
Hello all,
I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the
structure from scratch. I have converted PDB to mol2 with openbabel and
submitted at Swissparam (http://swissparam.ch/) which returned a zip file
containing various files of the same name (.itp,
Hello,
I understand that .itp is a topology file. But the swissparam pack does not
have a .gro file. How do I create solvated.gro ? (which has to be used in
grompp)
Is there a way to convert .itp in .top and .gro ? GROMACS tutorial does not say
whether .itp can sustitute the other two.
From:
). Can anyone tell
me what all files do I need to edit (what kind of data do I need to look for,
to be more specific) in order to make the program recognize this new residue
?Thanks in advance for help.Regards,Ashish Bihani
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