On Wed, May 25, 2011, Sindrila Dutta banik wrote:
>
> I am generating a topology file and coordinate file from a PDB
> structure using xleap. As I load the corresponding topology file and
> coordinate file to VMD to visualize, it shows that the first residue
> (a GLU residue) of the protein is having few very large bonds extended
> in space (these bonds are obviosuly wrong bonds).
There is not enough information present to help. What long bonds are they?
If they are only a "very few" you should be able to examine each on, compare
to the pdb file, and try to figure out what is happening.
> I did not put the
> N terminal residue (GLU) as NGLU and C terminal residue (a PRO) as CPRO
> (I should have done it as per manual) because whenever I put NGLU and
> CPRO in the pdb, a message appears during the loading in xleap that
> these residues are not in residue template.
First, it is *not* generally necessary to change the N and C terminal residues
in the PDB file, since the leaprc file does it for you. In fact, it is
dangerous to do so, since there are only three columns for the residue name
in a pdb file.
>
> How to resolve this?
We need more information. If you can't figure it out, you will need to post
a pdb file that doesn't work, and the *exact* commands you used to load it
into LEaP.
....dac
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Received on Wed May 25 2011 - 07:30:03 PDT
