hi
pdb4amber does not work with modified amino acid yet.
https://github.com/Amber-MD/pdb4amber/issues/46
It only uses standard resname:
https://github.com/Amber-MD/pdb4amber/blob/master/pdb4amber/residue.py#L75
Hai
On Tue, Sep 12, 2017 at 2:18 PM, Rajarshi Roy <phd1701171011.iiti.ac.in>
wrote:
> Dear amber users and developers,
>
> I am trying to simulate one modified peptide chain which is two leucine
> residue joined by a succinic acid. I created that structure and visually it
> is not showing any kind of discrepancy or gaps.But when I loaded this
> structure in tleap for solvation it is showing gap and also failed to
> generate prmtop file.So I tried pdb4amber for this , but it is also
> showing same kind of error and created some peculiar bonding.
>
> $ pdb4amber -i peptide.pdb -o peptide_clean.pdb
>
> ==================================================
> Summary of pdb4amber for: peptide.pdb
> ===================================================
>
> ----------Chains
> The following (original) chains have been found:
> A
>
> ---------- Alternate Locations (Original Residues!))
>
> The following residues had alternate locations:
> None
>
> ---------- Gaps (Renumbered Residues!)
> gap of 6.114874 A between LEU 1 and LEU 2
> gap of 9.126924 A between LEU 2 and LEU 4
>
> ---------- Mising heavy atom(s)
>
> None
>
> Can anyone have any suggestion?
> I also attached both the pdb file here.
>
> Thanks in advance
> --
>
> with regards
> Rajarshi Roy
>
> PhD Research Scholar
> Biosciences and Biomedical Engineering
> Indian Institute of Technology, Indore
> India
>
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Received on Tue Sep 12 2017 - 19:00:02 PDT
