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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Received on Tue Sep 12 2017 - 20:00:03 PDT
