Hello Dr. Anselm Horn,
Thanks a lot. Indeed, it is the visualization issue.
I only used vmd to check the pdb file as my equilibration failed.
Yeah, I checked with vim on the pdb file, my guess is that as the
residue number
gets larger, the coordinates fields shift a little (by one), making
those water molecules visualized abnormally.
Then I check the topology and coordinates file, it looks fine.
All the best,
Qinghua
On 2/10/22 09:08, Dr. Anselm Horn wrote:
> Qinghua,
>
> maybe it is just a visualization issue.
>
> What file did you use for visualization?
> If it was a pdb file, you could have run into file format problems due
> to the size of your system; you probably can tell from a simple
> inspection of that file in a text editor.
>
> Do you obtain the same picture with the crd/top file pair you generated
> via leap?
>
> Best regards,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
>
> On 02/10/2022 12:23 AM, Qinghua Liao wrote:
>> Hello,
>>
>> I have a very big protein, ~2400 AA, and I tried to do the solvation with
>>
>> solvatebox mol TIP3PBOX 10 iso
>>
>> But it failed, it does not look normal, as attached. Any suggestion?
>> Thanks!
>>
>>
>> All the best,
>> Qinghua
>>
>>
>> _______________________________________________
>> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 10 2022 - 02:00:02 PST
