On Thu, 2015-01-15 at 05:08 -0800, Shreeramesh wrote:
> Dear all,
>
> I ran a tleap using pdb file and I got a following error. Can you please
> suggest to solve the following error. I also attached the script for tleap
> and pbd of protein for your kind attention.
>
>
> Loading PDB file: ./rec.pdb
> -- residue 333: duplicate [ C] atoms (total 2)
> -- residue 333: duplicate [ CA] atoms (total 2)
> -- residue 333: duplicate [ N] atoms (total 2)
> -- residue 333: duplicate [ O] atoms (total 2)
> -- residue 334: duplicate [ C] atoms (total 2)
> -- residue 334: duplicate [ CA] atoms (total 2)
> -- residue 334: duplicate [ CB] atoms (total 2)
> -- residue 334: duplicate [ N] atoms (total 2)
> -- residue 334: duplicate [ O] atoms (total 2)
> -- residue 177: duplicate [ C] atoms (total 2)
> -- residue 177: duplicate [ CA] atoms (total 2)
> -- residue 177: duplicate [ CB] atoms (total 2)
> -- residue 177: duplicate [ CG] atoms (total 2)
> -- residue 177: duplicate [ N] atoms (total 2)
> -- residue 177: duplicate [ O] atoms (total 2)
> -- residue 177: duplicate [ OD1] atoms (total 2)
> -- residue 177: duplicate [ OD2] atoms (total 2)
> -- residue 204: duplicate [ C] atoms (total 2)
> -- residue 204: duplicate [ CA] atoms (total 2)
> -- residue 204: duplicate [ CB] atoms (total 2)
> -- residue 204: duplicate [ CD] atoms (total 2)
> -- residue 204: duplicate [ CG] atoms (total 2)
> -- residue 204: duplicate [ N] atoms (total 2)
> -- residue 204: duplicate [ O] atoms (total 2)
> -- residue 204: duplicate [ OE1] atoms (total 2)
> -- residue 204: duplicate [ OE2] atoms (total 2)
> -- residue 478: duplicate [ CA] atoms (total 2)
> -- residue 478: duplicate [ CB] atoms (total 2)
> -- residue 478: duplicate [ CD] atoms (total 2)
> -- residue 478: duplicate [ CG] atoms (total 2)
> -- residue 478: duplicate [ OE1] atoms (total 2)
> -- residue 478: duplicate [ OE2] atoms (total 2)
>
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
>
> Unknown residue: ASN number: 0 type: Terminal/beginning
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: SER number: 1 type: Nonterminal
> Unknown residue: PRO number: 2 type: Nonterminal
> Unknown residue: ILE number: 3 type: Nonterminal
These error messages indicate that the standard amino acids could not be
found by tleap. What this means is that the standard residue template
libraries were not loaded.
I noticed that your script started with the command:
source leaprc.ff99SB
If you try to run this in tleap using AmberTools 14 (but you never did
say what version of Amber you were using), you will get this message:
> source leaprc.ff99SB
Could not open file leaprc.ff99SB: not found
This is because ff99SB has been superseded by "better" force fields
(specifically, ff12SB and ff14SB). I suspect if you go back to your
leap.log file, you will see that error message written there. So when
the rest of the commands were executed, tleap couldn't find the residues
(which *should* have been loaded by leaprc.ff99SB) and so resulted in
this error.
So the solution is this: replace "ff99SB" with a newer force field, like
"ff14SB". If you MUST use ff99SB (e.g., for comparison with past
results, for instance), then change "leaprc.ff99SB" to
"oldff/leaprc.ff99SB".
Hope this helps,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 15 2015 - 06:30:04 PST
