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 - 11:30:02 PDT
