Hi,
If you have the original PDB or input structure you started with and know
the conditions (box size, ions, etc), you can try to remake it? Since you
know the number of atoms of your peptide/everything else, feeding it into
tleap again with water will give you a N waters, which you can then
hand-edit it down to the correct number of water atoms. Then you should be
able to load it into cpptraj/VMD, and resave it as the 'correct' prmtop.
It's not a neat solution, but I've had it work in a quick pinch when I lost
the original prmtop and had to try to recreate it.
Best,
Kenneth
On Fri, Feb 5, 2021 at 4:56 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 - 07:30:02 PST
