Dan,
Thanks for the information.
Merry Christmas!
Jim
James Kress Ph.D., President
The KressWorks® Institute
An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
“ENGINEERING THE CURE” ©
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-----Original Message-----
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Thursday, December 23, 2021 9:23 AM
To: James Kress <jimkress_58.kressworks.org>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] prmtop file generated with CLOSEST in cpptraj
Hi,
On Wed, Dec 22, 2021 at 7:05 PM James Kress <jimkress_58.kressworks.org> wrote:
>
> Why is this prmtop file generated when cpptraj CLOSEST command is
> used? Is
The 'closest' command will retain only the specified number of solvent molecules (removing the rest), so the resulting topology will differ from the original topology. The new topology corresponds to the new pared-down system.
> it required for any future calculations on the system to which CLOSEST
> is
It's only necessary if you want to e.g. process an output trajectory generated after the 'closest' command. If you use an output trajectory format that has some topology information (like mol2) the topology generated by 'closest' may be unnecessary (although it won't have things like angle/nonbond/etc parameters).
-Dan
> applied?
>
> Any insight would be appreciated.
>
> Thanks.
>
> Jim
>
> James Kress Ph.D., President
> The KressWorksR Institute
> An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
> "ENGINEERING THE CURE" C
> (248) 573-5499
>
> Learn More and Donate At:
> Website: http://www.kressworks.org
>
> Confidentiality Notice | This e-mail message, including any
> attachments, is for the sole use of the intended recipient(s) and may
> contain confidential or proprietary information. Any unauthorized
> review, use, disclosure or distribution is prohibited. If you are not
> the intended recipient, immediately contact the sender by reply e-mail
> and destroy all copies of the original message.
>
>
> _______________________________________________
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Received on Thu Dec 23 2021 - 11:30:03 PST
