How did you build the prmtop? Can you give more details about that step?
On Fri, Feb 5, 2021, 4:55 AM Violeta Burns Casamayor <vb0009.mix.wvu.edu>
wrote:
> 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 - 04:00:02 PST
