Thank You so much for your response!
Here I have attached the topology and coordinate file I am using.
On Mon, Nov 16, 2020 at 12:53 AM Giorgos Lambrinidis <
lamprinidis.pharm.uoa.gr> wrote:
> Dear Ankita,
>
> The error is related to the atom numbering of the two ligands. Can you
> attach the topology and coordinate file you utilized for further
> inspection?
>
> Dr. George Lamprinidis
>
> > Dear users,
> >
> > It's a gentle reminder.
> > Any suggestions or comments would be very helpful.
> > Thank you in advance!
> >
> > Kind regards
> > Ankita Tripathi
> >
> > On Thu, Nov 12, 2020, 6:49 PM Ankita Tripathi <at194.snu.edu.in> wrote:
> >
> >> Dear Users,
> >> I am very new to thermodynamic integration. I have successfully done the
> >> TI tutorial for amber that is available at
> >> http://ambermd.org/tutorials/advanced/tutorial9 without any problems or
> >> warnings.
> >>
> >> Now I started implementing it on my system which includes one protein
> >> and
> >> two ligands Glutamyl phosphate(RGP) and N-Acetyl glutamyl
> >> phosphate(UNK),
> >> basically, I wanted to calculate the relative free energy.
> >>
> >> I have done the first step in the setup that is Setting up the
> >> vdW+bonded
> >> transformation step without any issue after that in the second step
> >> Running
> >> MD to provide sane starting coordinates I am getting the following error
> >> in
> >> the minimization step
> >> default_name
> >> Mask !:WAT & !.H=; matches 36 atoms
> >> TI Mask 1 :RGP; matches 22 atoms
> >> TI Mask 2 :UNK; matches 26 atoms
> >> TI region 1: 3627 atoms
> >> TI region 2: 3631 atoms
> >> SC Mask 1 :RGP.H1,HN1,HN2; matches 3 atoms
> >> SC Mask 2 :UNK.O5,C6,C7,H6,H7,H8,H9; matches 7 atoms
> >> Error : Atom 16 does not have match in V1 !
> >>
> >> I followed all the key points that are all the common atoms of ligands
> >> in
> >> input files have identical starting coordinates, appear in the same
> >> order,
> >> share the same atom names.
> >> I am attaching all the required input files.
> >>
> >> Any advice, suggestions would be of great help to me!
> >> Thank You in advance.
> >>
> >> Kind Regards
> >> Ankita Tripathi
> >>
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> >
>
>
> --
> “Good judgement is the result of experience and experience the result of
> bad judgement.”
>
> ― Mark Twain
>
> ---------------------------------------------
> Dr George Lambrinidis
> Researcher & Laboratory Assistant Staff
> School of Health Sciences
> Faculty of Pharmacy
> National & Kapodistrian University of Athens
> Greece
> tel: +30 2107274304
> +30 2107274521
> fax: +30 2107274747
> e-mail: lambrinidis.pharm.uoa.gr
> geolampr.gmail.com
> ---------------------------------------------
>
>
>
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Received on Sun Nov 15 2020 - 12:00:02 PST
