Thank you Elvis for your response. However, the protein complex I am using
contains a protein as the receptor and a small peptide as the ligand. Both
are different units but connected by a single bond.
I wanted to establish a bond between the ligand and protein by the bond
command
"bond RN2.401.C25 CYS.145.SG <
http://cys.145.sg/> - "
The bond command mentioned in the amber
Manual is to make a bond between two atoms of the same UNIT, however in our
case it is the two different units (between a protein as the receptor and a
peptide as a ligand.)
Please suggest me how to deal with it.
Thank you for your kind suggestions.
Best regards
Priyanka Purohit
On Sat, 3 Jul, 2021, 3:59 PM Elvis A F Martis, <martiseaf.elvismartis.in>
wrote:
> Hi
> the bond command you are using is incorrect.
> It should look something like this
>
> "bond RN2.401.C25 RN2.145.SG" (without quotes)
>
>
> On Sat, 3 Jul 2021 at 15:18, PRIYANKA PUROHIT <p.purohit.bioinfo.gmail.com
> >
> wrote:
>
> > Dear Sir,
> > I am Priyanka Purohit, a research scholar of Berhampur University,
> Odisha,
> > India. I have a query regarding the single covalent bond formation in a
> > protein-ligand complex using the AMBER18 tleap command ' bond RN2.401.C25
> > CYS.145.SG - ' . But I am having certain errors ' Error: bond: Argument
> #1
> > is type String must be of type: [atom] usage: bond <atom1> <atom2>
> [order]
> > ' while using it. So, I need your kind suggestions to know the exact
> > process to build a single covalent bond by using AMBER18.
> > Thanking you in advance, Waiting for your kind reply.
> > Regards,
> > Priyanka Purohit ,
> > Research Scholar.
> > Berhampur University,
> > Odisha,India.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Best Regards
> Elvis
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Received on Mon Jul 19 2021 - 05:30:02 PDT
