Hi,
I attached my Log file here. I am using gaff2 for succenic acid.
On Wed, Sep 13, 2017 at 8:06 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> ok, so I read your message more carefully and pdb4amber does not contribute
> to the issue.
>
> The original pdb has below HETATM and I think it's trouble (I will let
> others to comment)
>
> May be change "HETATM" to "ATOM"? (shot in the dark)
>
> HETATM 41 C3 SIN A 3 1.583 1.736 -1.802 1.00 0.00
> C
>
> HETATM 42 C2 SIN A 3 0.495 0.549 -1.722 1.00 0.00
> C
>
> HETATM 43 C1 SIN A 3 -1.015 0.928 -1.727 1.00 0.00
> C
>
> HETATM 44 O1 SIN A 3 -1.319 2.105 -1.816 1.00 0.00
> O
>
> HETATM 45 C4 SIN A 3 3.063 1.209 -1.833 1.00 0.00
> C
>
> HETATM 46 O3 SIN A 3 3.198 0.012 -1.665 1.00 0.00
> O
>
> HETATM 47 H31 SIN A 3 1.443 2.404 -0.928 1.00 0.00
> H
>
> HETATM 48 H32 SIN A 3 1.371 2.308 -2.732 1.00 0.00
> H
>
> HETATM 49 H21 SIN A 3 0.693 -0.077 -0.829 1.00 0.00
> H
>
> HETATM 50 H22 SIN A 3 0.637 -0.097 -2.620 1.00 0.00
> H
>
>
> Hai
>
> On Tue, Sep 12, 2017 at 9:37 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> _______________________________________________
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>
--
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 - 23:00:02 PDT
