On Sat, Dec 1, 2012 at 2:12 AM, Shubhadip Das <d.shubhadip.yahoo.com> wrote:
> Dear Amber Users,
> I have a
> pdb file of a protein which has residue name "MOL" for each residue.
> When I tried to load it in xleap with force field ff99SB following lines
> appeared in the xleap window. Will you please let me know how should I
> proceed to avoid this problem.
>
LEaP requires every residue be named 'correctly'. That is, there *must* be
a library that provides a residue template with the same residue name as
any residue you attempt to load into a structure. In this case, all
residues in your PDB file should *only* be named MOL if they are all the
same, custom residue. If this is the case, then you will have to generate
a residue template (either a mol2 file or something related, like mol3 or
an Amber OFF file).
If they are standard amino acids, then they should be named with the
appropriate 3-letter sequence (with some exceptions for different
protonation states). In this case, don't use an editor that clobbers the
residue names.
See the Amber tutorials .
http://ambermd.org/tutorials for more help.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Dec 01 2012 - 07:00:02 PST
