> On Apr 9, 2015, at 7:15 AM, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
> Hi All,
> I have prepared prmtop and inpcrd files as discussed in a recent thread
> (can't find the link in the archive yet).
> But I am getting strange warnings from tleap that there are large bonds
> between atoms of the same residues (protein and ligand).
> I have checked the coordinates for a couple of them and this doesn't look
> to be the case.
> Can you please take a look and suggest me if these are due to bad pdb
> structure or some other error?
You would know your system better than we would. You are getting errors because some of the residues that are adjacent in sequence are 20+ angstroms apart from one another. However, tleap will always try to connect two adjacent amino acid residues (or nucleic acid residues) that are not separated by a TER card.
So if your protein has multiple chains, you need to make sure that there is a TER card after the last atom in each chain so that tleap doesn’t try to bond the two chains together.
If there *aren’t* multiple chains, then your PDB looks like it has gaps in the sequence that you might have to fill in with some homology modeling tool or other PDB massager (I think PDBFixer will do this for you: https://github.com/pandegroup/pdbfixer <https://github.com/pandegroup/pdbfixer>).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Apr 09 2015 - 04:30:07 PDT
