The exact message while trying to visualise on VMD is: Problem reading CRD
file
I was trying to load the remd.mdcrd.001 file along with a top file.
Also, when I tried to extract temperature trajectories using the script (
extract_300k_traj.x
<
http://ambermd.org/tutorials/advanced/tutorial7/files/extract_300k_traj.x>),
I am getting the distance file as output but not any trajectory file. It
does not show any error.
Please advise
Thank you
Suchetana
On Sun, Jun 26, 2022 at 1:04 PM Suchetana Gupta <suchetana.gupta.gmail.com>
wrote:
> I have run a regular MD on the same cyclic peptide and it runs fine and I
> can do all visualisations and stuff. However when I generate the REMD
> trajectories using the same structure, VMD gives the error of cannot load
> trajectory.
> Thanks
> Suchetana
>
> On Sun, Jun 26, 2022 at 12:58 PM David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Sun, Jun 26, 2022, Suchetana Gupta via AMBER wrote:
>>
>> >Is there any updated tutorial for running REMD simulations? I am trying
>> to
>> >do REMD simulations for cyclic peptides using Amber20. I have followed
>> the
>> >tutorial...
>> >Somehow, I am unable to visualise the trajectory after following these
>> >steps. The trajectory does not load in VMD. Any solution for it?
>>
>> There should be no particular connection between using REMD, and having
>> your
>> system be a cyclic peptide.
>>
>> 1. does your system run OK without REMD, and can you visualize the
>> trajectories?
>>
>> 2. What is the exact error message you get in VMD? At what stage of the
>> process?
>>
>> ...thx...dac
>>
>>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 04 2022 - 13:33:26 PDT
