Dear Amber users,
I’m in a pickle. I have 15 simulations of a peptide in solution that have completed without a problem but when I went to do analysis I found out that the prmtop have the whole protein as residue 1, and that there are no residue names for any of the protein residues (instead I have *****). I have tried adding this info to the prmtop, and vmd is able to detect a protein, but there is no secondary structure information and therefore useless for analysis). I have tried obtaining a mol2 and pdb files and modifying those, and then use them in tleap to get a new prmtop, but tleap seems to not be able to recognize the water atoms nor does it detect the bond information between them (even with the frcmod file loaded).
I really don’t know what else to try and I don’t want to throw away 15 ish microseconds of simulations. Has anyone ever encounter this problem and be able to solve it? Or does anyone have any ideas as to what I can try?
Any help is appreciated!
Thank you.
Violetta Burns
PhD student
Mertz Group
vb0009.mix.wvu.edu
WVU Department of chemistry
"Every great and deep difficulty bears in itself its own solution. It forces us to change our thinking in order to find it." - Niels Bohr
“You do not really understand something unless you can explain it to your grandmother.” - Albert Einstein
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Received on Fri Feb 05 2021 - 02:00:02 PST
