AMBER Archive (2009)

Subject: Re: [AMBER] Problem with nonstandard residues

From: moitrayee_at_mbu.iisc.ernet.in
Date: Tue May 19 2009 - 11:47:38 CDT

Thank you very much. Changing the residue numbers of TSB to 1002 for all the
atoms solved the problem and the prmtop and prmcrd files are built. Also I am
greatful for the desc suggestion.
Thanks once again.

Sincere Regards,
Moitrayee

> On Tue, May 19, 2009, moitrayee_at_mbu.iisc.ernet.in wrote:
>
>> Thanks a lot for the mail. I have already renamed the atoms in the pdb file
>> 1QF6_TSB.pdb according to the atom names in TSB.in. The previous error showed
>> after these modifications. I am attaching the pdb and prepi files.
>> It would be great if you please suggest what might be the problem.
>
> You pdb file doesn't give all of the TSB atoms the same residue number:
>
> ...
> ATOM 13068 C14 TSB A2002 36.902 77.357 48.490 1.00 11.51
> ATOM 13069 N6 TSB A2002 34.178 75.035 49.798 1.00 11.95
> ATOM 13070 C12 TSB A2002 35.226 75.511 48.919 1.00 11.94
> ATOM 13071 C13 TSB A2002 36.006 76.687 49.542 1.00 11.60
> ATOM 13072 O9 TSB A2002 35.092 77.677 50.036 1.00 11.90
> ATOM 13073 C11 TSB A2002 36.162 74.359 48.709 1.00 12.30
> ATOM 13074 O8 TSB A2002 36.002 74.001 49.999 1.00 12.85
> ATOM 6829 P1 TSB A1002 37.529 72.382 47.370 1.00 38.54 P
> ATOM 6830 O6 TSB A1002 37.295 70.912 47.274 1.00 38.04 O
> ATOM 6831 O7 TSB A1002 37.157 73.261 46.244 1.00 39.13 O
> ATOM 6832 O3 TSB A1002 36.811 72.878 48.694 1.00 37.08 O
> ATOM 6833 O2 TSB A1002 39.069 72.659 47.633 1.00 40.09 O
> ATOM 6834 C10 TSB A1002 39.578 74.002 47.702 1.00 40.09 C
>
>
> Note that the first 7 atoms have a different residue number than the atoms
> that follow. Leap is confused into thinking that there are two residues here.
> You need to fix up the pdb file so that the TSB residue all looks like it has
> the same residue number.
>
> [Aside: how to find something like this yourself: try to load just the TSB
> part of the pdb file, e.g. with "x = loadpdb TSB.pdb". Then use the "desc"
> command, e.g. "desc x.1". You will see two residues where there should only
> be one. Breaking a pdb file into smaller pieces and using the desc command is
> a common debugging strategy.]
>
> ...dac
>
>
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