I would suggest isolating some of these variables. First try the
simulations without the nonstandard residues but everything else the same.
Then you can try to change only the amber version, or solvent, or machine
where you run it.
On Nov 16, 2017 10:12 AM, "Chetna Tyagi" <cheta231.gmail.com> wrote:
> Dear amber users,
>
> I have been trying to run simple explicit solvent simulation on a Amber14
> machine while using AmberTools16 generated input files.
>
> I generate the topology and run Minimization and heating steps and finally
> submit the job to the Amber14 machine. Also, my peptide contains
> non-standard residues like AIB and D-isovaline.
>
> This results in a distorted peptide and water molecules. I have attached a
> picture of the peptide below. I also tried with minimization and heating
> steps using Amber14 and the result was the same in both TIP3P and MEOH
> solvents.
>
> The simulation runs fine and shows no error messages but the output is
> distorted.
>
> Also, I have used the same strategy for implicit simulation carrying out
> minimization on AmberTools16 and production run on Amber14 and it turns out
> to be fine always.
>
> I have also checked running the production on AmberTools16 and this also
> results in normal output.
>
> I don't understand whether it is really the matter of using two different
> versions of Amber or something else. I would be grateful if someone can
> guide me towards the right direction.
>
> Comparing the input files I don't find huge difference between AmberTools16
> and Amber14
>
>
> *Note: *I am trying to use Amber14 available on the local server. That is
> the MPI version and is the latest one available.
>
> [image: Inline image 3]
>
>
>
>
> --
> Best wishes
> Chetna
>
> _______________________________________________
> 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
Received on Thu Nov 16 2017 - 08:30:02 PST
