In tleap script, I have write savedpb, and it built a new pdb. When I open
this pdb file, it still contain residue number 291 which is Alanin (residue
number protein) and 292 is my ligand UNL. But, in leap log file, it written
:
Added missing heavy atom: .R<CALA 296>.A<OXT 11>
Added missing heavy atom: .R<UNL 297>.A<C1 2>
Added missing heavy atom: .R<UNL 297>.A<C2 4>
Added missing heavy atom: .R<UNL 297>.A<C3 5>
total atoms in file: 2337
Leap added 2301 missing atoms according to residue templates:
4 Heavy
2297 H / lone pairs
This is in complex pdb file:
ATOM 4616 HB1 ALA 291 -14.075 10.706 15.263 1.00 0.00
ATOM 4617 HB2 ALA 291 -15.521 9.686 15.452 1.00 0.00
ATOM 4618 HB3 ALA 291 -14.216 9.184 14.351 1.00 0.00
ATOM 4619 C ALA 291 -16.264 11.964 14.139 1.00 0.00
ATOM 4620 O ALA 291 -17.485 11.983 13.973 1.00 0.00
ATOM 4621 OXT ALA 291 -15.715 12.883 14.743 1.00 0.00
TER
ATOM 4622 C UNL 292 8.692 -1.913 -8.224 1.00 0.00
ATOM 4623 C1 UNL 292 8.830 -1.676 -9.741 1.00 0.00
ATOM 4624 Br UNL 292 8.566 0.678 -6.842 1.00 0.00
ATOM 4625 C2 UNL 292 9.838 -2.762 -7.626 1.00 0.00
ATOM 4626 C3 UNL 292 9.491 -4.261 -7.565 1.00 0.00
ATOM 4627 H UNL 292 7.790 -2.470 -8.077 1.00 0.00
ATOM 4628 H1 UNL 292 8.783 -2.614 -10.253 1.00 0.00
ATOM 4629 H2 UNL 292 9.769 -1.204 -9.943 1.00 0.00
ATOM 4630 H3 UNL 292 8.035 -1.044 -10.077 1.00 0.00
ATOM 4631 H4 UNL 292 10.040 -2.415 -6.634 1.00 0.00
ATOM 4632 H5 UNL 292 10.690 -2.651 -8.263 1.00 0.00
ATOM 4633 H6 UNL 292 8.640 -4.405 -6.933 1.00 0.00
ATOM 4634 H7 UNL 292 10.324 -4.805 -7.170 1.00 0.00
ATOM 4635 H8 UNL 292 9.269 -4.616 -8.549 1.00 0.00
TER
so what the residue number ligand that I use for analysis? I still confuse.
Is 297 ligand residue number or not?
On Tue, Jul 4, 2017 at 10:49 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Best to copy/paste actual output.
>
> Residues get numbered sequentially when leap builds a model, and pdb
> residue numbers are lost.
>
> One way to see the new residue numbers is to savepdb in leap, so you
> have a pdb to go from.
>
> Bill
>
>
> On 7/4/17 8:00 AM, NADIA RAHMAH wrote:
> > Hello. I run MD for protein complex docked, in complex pdb file
> > (preparation result), there are 292 residu number, which 1-291 are
> protein
> > (receptor) amino acid residue and residue number 292 is the ligand name
> > UNL. When I run preparation solvated box and without no box, there are
> > written like:
> > there is bond 297 <UNL> <Br>
> > There is bond 297 <UNL> <H>
> >
> > It written UNL in 297 residu. I confuse how Amber read my protein residue
> > number? How I can see the list of all residue number, I have to know what
> > is residue number of the ligand, I need to fix it because I want analyst
> it
> > with RMSD, MMPBSA, etc.
> > I hope anybody can help me. Thanks
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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>
--
*Regards,*
*Nadia Rahmah*
*Department of Physics Undergraduate Student - 2013Bogor Agricultural
University*
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Received on Tue Jul 04 2017 - 17:30:02 PDT
