a detail command + output log message from tleap would be helpful.
by the way, do you have force field for SIN yet? if not, tleap can't not
understand it.
Hai
On Tue, Sep 12, 2017 at 11:56 PM, Rajarshi Roy <phd1701171011.iiti.ac.in>
wrote:
> Hi,
>
> I previously did this by changing HETATM to ATOM but I am getting same
> error.
>
> 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
> > >>
> > >>
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> 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 - 21:30:02 PDT
