Dear Dr. Lambrinidis,
My problem has been solved.
Thank you so much.
Kind regards
Ankita Tripathi
On Mon, Nov 16, 2020 at 1:51 PM Giorgos Lambrinidis <
lamprinidis.pharm.uoa.gr> wrote:
> Dear Ankita,
>
> Check again the numbering and pdb labels in your pdb files.
> For inistance i see HG2 in RGP1 has been renamed HG1 in UNK2 and vice
> versa.
>
>
> Best
> George
>
> > 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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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >> --
> >> “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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> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> “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 Tue Nov 17 2020 - 04:30:02 PST
