I named sugar portion as 0GB to follow GLYCAM naming scheme and the rest of
the ligand as UNK because GLYCAM doesnt have triple bond parameters. Is it
the correct way to handle such ligands?
On Thu, Oct 18, 2018 at 1:00 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> You have
>
> ...
>
> ATOM 19 O21 0GB 1 6.500 2.115 -1.901 1.00
> 0.00 O
> ATOM 20 H22 0GB 1 5.632 1.856 -1.567 1.00
> 0.00 H
> ATOM 21 O23 0GB 1 5.282 -0.385 -2.359 1.00
> 0.00 O
> ATOM 22 H24 0GB 1 4.824 0.294 -1.828 1.00
> 0.00 H
> ATOM 23 C25 UNK 2 5.022 3.662 -9.358 1.00
> 0.00 C
> ATOM 24 N26 UNK 2 4.804 4.566 -10.043 1.00
> 0.00 N
> ATOM 25 C27 UNK 2 6.665 1.899 -8.925 1.00
> 0.00 C
> ATOM 26 H28 UNK 2 7.461 2.619 -8.729 1.00
> 0.00 H
> ATOM 27 H29 UNK 2 6.653 1.658 -9.992 1.00
> 0.00 H
> ATOM 28 H30 UNK 2 6.870 0.983 -8.368 1.00
> 0.00 H
> ATOM 29 C31 UNK 2 4.175 1.460 -8.687 1.00
> 0.00 C
> ATOM 30 H32 UNK 2 4.068 1.209 -9.746 1.00
> 0.00 H
> ATOM 31 H33 UNK 2 3.228 1.862 -8.322 1.00
> 0.00 H
> ATOM 32 H34 UNK 2 4.409 0.545 -8.139 1.00
> 0.00 H
> ATOM 33 O35 UNK 2 5.381 2.953 -7.150 1.00
> 0.00 O
> ATOM 34 C36 UNK 2 5.309 2.491 -8.473 1.00
> 0.00 C
>
> And you have a I1-lig.prep for the 0GB residue:
>
> This is a remark line
> molecule.res
> 0GB INT 0
> CORRECT OMIT DU BEG
> 0.0000
>
> (The atom naming follows an odd numbering scheme.)
>
> But you have no prep file for the UNK residue. Why is that? I'd give it
> a more descriptive name if it's supposed to be there.
>
> Bill
>
> On 10/18/18 12:18 AM, senal dinuka wrote:
> > As per your suggestion I prepared the prep file and separately carried
> out
> > tleap for the ligand portion only. connectivity and naming for sugar
> > portion named 0GB is shown to be available but for the portion of ligand
> > named UNK, it is still missing. Here I have attached the extracted
> ligand,
> > prep file and its tleap script. Is it possible to work with two residue
> > names like here. If so am I doing it the correct way? I appreciate your
> > suggestion
> >
> > Regards,
> >
> > On Thu, Oct 18, 2018 at 10:16 AM Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> > FATAL: Atom .R<UNK 468>.A<C36 12> does not have a type.
> >>
> >> Looks like you didn't create a template for your residue? See tutorials
> >> (biotin might be good). Res/atom names must match between template and
> pdb.
> >>
> >> > Could not find bond parameter for: Cg -
> >>
> >>> Could not find angle parameter: Cg - Cg -
> >> It looks like a blank-space atom type might have slipped through
> >> Interpol's net. Maybe if you fix the residue template, you will be able
> to
> >> fix that from the experience.
> >>
> >> Bill
> >>
> >> On 10/17/18 9:34 PM, senal dinuka wrote:
> >>> I have been trying to generate prmtop and inpcrd files for the below
> >>> mentioned receptor/ligand complex. The ligand is a TS structure hence
> the
> >>> weird bond lengths. I was told to use GLYCAM for the sugar portion and
> >>> separate frcmod for the cyanogenic part of the ligand since GLYCAM
> doesnt
> >>> offer parameters for the later. Hence I generated a l1.frcmod with bcc
> >>> charge scheme through antechamber and parmchk modules with default
> >> options.
> >>> frcmod seem to be lack in bond and angle properties. And thus the leap
> >>> results in error I assumed. I appreciate your guidance regarding the
> >> matter.
> >>> Thank you
> >>> P.S I have attached the complex, ligand as well as frcmod and leap
> >> script I
> >>> used
> >>>
> >>>
> >>>
> >>>
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> >
> >
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--
D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Rajagiriya
Sri Lanka
+94 77 627 4678
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Received on Thu Oct 18 2018 - 01:00:02 PDT
