Well, in that case, combine the two units using the "combine" command in
leap.
> com = combine {unit1 unit2}
Then you can use "com" as the new unit
> bond com.401.C25 com.145.SG <http://rn2.145.sg/>
PLEASE NOTE, after combining the units, the residue numbers will change,
use the "desc" command to know what all has changed.
Accordingly, modify your "bond" command.
I hope this helps.
On Mon, 19 Jul 2021 at 17:48, PRIYANKA PUROHIT <p.purohit.bioinfo.gmail.com>
wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> 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 - 06:00:02 PDT
