On Sat, Feb 21, 2015 at 10:41 AM, Shreeramesh <shreeramesh.gmail.com> wrote:
> Dear Sir,
>
>
> After running tleap, "com_solvated.pdb" file was generated, in this, the
> bond between carbon and chlorine is missing with the following error
> message
>
This has been said numerous times on this thread by both me and others,
but I will reiterate. The PDB files printed by LEaP does not contain ANY
bond information. It never has, it likely never will. This does *NOT*
mean that the bond was deleted. It simply means that you should not use
images of PDB files generated by VMD or Chimera to determine what bonds
tleap added to a topology file. The only reason the bond *seems* to be
broken is that visualization programs draw bonds based on how far away
atoms are from each other, and the atoms are too far away in your PDB file.
Look at the *topology* file to see if a bond exists. NOT the PDB file.
In other visualization program, the atoms are changed to carbon though
> there are chlorine in text file
>
You are putting too much stock in what visualization programs tell you.
The only information that matters to Amber is what is stored in the
topology file, so you should use ParmEd to look specifically at the
topology file and see if bonds and stuff are present. It will also tell you
what element each atom is if you use the "printDetails" command.
> I also attached frcmod file and com_solvated.pdb for your kind attention
> and request you to kindly help me in this regard
>
> Warning in tleap:
> hecking 'LIG'....
> Warning: Close contact of 1.435025 angstroms between .R<CLM 1>.A<C5 1> and
> .R<CLM 1>.A<O5 13>
> Warning: Close contact of 1.487896 angstroms between .R<CLM 1>.A<C5 1> and
> .R<CLM 1>.A<C6 15>
>
Again, these are warnings, not errors. They indicate that your starting
structure might be strained. They are unrelated to any of the concerns
you are reporting here.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Feb 21 2015 - 10:00:02 PST
