After further attempts this seems to be an issue with the way MOE alters
input coordinates. VMD gives the expected behavior with defaults - sorry
for the implied doubt that this had not been tested!
On Wed, Jun 29, 2022, 8:21 AM Brian Radak <brian.radak.gmail.com> wrote:
> This is the latest release - AmberTools22
>
> I've tried both .mrc and .ccp4 - I should probably check .dx too. I'm
> using default boundary conditions (I assume open) with a small-ish buffer -
> here are the relevant command-line options:
>
> --buffer 7.0 --grdspc 0.35,0.35,0.35 --volfmt mrc --tolerance 1e-05
>
> It might be worth mentioning that I'm _only_ interested in the water
> density around a ligand binding site.
>
> Brian
>
> On Tue, Jun 28, 2022, 7:37 PM tluchko <tluchko.protonmail.com> wrote:
>
>> Hi Brian,
>>
>> What version of AmberTools are you using? Are you using open or periodic
>> boundaries? Is the output MRC or CCP4 format?
>>
>> Tyler
>>
>>
>> Sent with Proton Mail secure email.
>>
>> ------- Original Message -------
>> On Tuesday, June 28th, 2022 at 11:04 AM, Brian Radak via AMBER <
>> amber.ambermd.org> wrote:
>>
>>
>> > Hopefully Tyler sees this.
>> >
>> > I'm having a bit of a hard time visualizing grid output from
>> > rism3d.snglpnt. Everything seems to be translated relative to the input
>> > protein, which I realized is exactly what the manual says the default
>> > behavior should be. I tried the (discouraged) --centering 0 option, but
>> > this seemed to cause the densities to wrap around the grid in weird
>> ways,
>> > so that's probably not what I'm looking for. I don't recall having this
>> > issue with the old OpenDx file format, but I'm more than happy with the
>> > upgrade to .mrc otherwise.
>> >
>> > What's the recommended way to visualize densities around a protein? Is
>> > there a way to output the translated solute coordinates? Do I just need
>> to
>> > turn off centering and prepare my inputs more carefully? Something else?
>> >
>> > Regards,
>> > Brian
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Thu Aug 04 2022 - 13:33:48 PDT
