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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Received on Sat Nov 14 2020 - 12:00:02 PST
