Respected Team,
I hope you are doing well.
I am writing to follow up on my previous query sent on August 5th regarding
discontinuities observed in the .crd file (related to water molecules),
which are not visible in the .pdb file generated by tleap.
I kindly request your assistance in resolving this issue as soon as
possible, as it is affecting the energy minimization stage of my simulation
and impacting my ongoing research work. If this is related to periodic box
wrapping or visualization artifacts, please guide me on how to address it
correctly.
Thank you again for your support.
Best regards,
Yashika
PhD Scholar, Department of Chemistry
NSUT, Delhi
On Tue, Aug 5, 2025 at 3:48 PM YASHIKA . <yashika.phd23.nsut.ac.in> wrote:
> Respected Team
>
> I hope this message finds you well.
>
> I am currently working with the AMBER software as part of my
> research. While analyzing the .crd file (screenshot attached), I noticed
> discontinuities or breaks in the water molecules. However, the same issue
> is not observed in the .pdb file generated using the same leap.in file
> (screenshot attached). This discrepancy is likely causing problems in the
> energy minimization step.
>
> For your reference, the file paths are as follows:
>
> -
>
> *.crd file:* /home/leena/yashika/complex_final/with_184.crd
> -
>
> *tleap-generated .pdb file:* /home/leena/yashika/complex_final
> /tleap.pdb
>
> Could you please help me understand why this issue is occurring? Is it
> related to periodic box wrapping or a visualization artifact? Any
> suggestions on resolving it would be greatly appreciated.
>
> Thank you for your time and support.
>
> Best regards,
> Yashika
> PhD Scholar, Department of Chemistry
>
> NSUT, Delhi
>
>
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Received on Wed Aug 06 2025 - 04:00:03 PDT
