Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points

From: Matthew Guberman-Pfeffer <>
Date: Mon, 31 Jan 2022 14:16:36 -0500

Dr. Case,

The tutorial on extra points <> says,

 "With the addition of topology writing capabilities and a new format for encoding the extra points, these features of the system can start to become more permanent. The current master branch of pmemd and pmemd.cudasupport the upgraded topology format, and will be available to all users in Amber22. Users who need early access to this functionality should contact the developers.” [emphasis mine]

How do we place this request? I sent a message to the thread a few weeks ago on this issue as well and got no reply.


> On Jan 31, 2022, at 1:23 PM, David A Case <> wrote:
> *Message sent from a system outside of UConn.*
> On Wed, Jan 19, 2022, 王世玉 wrote:
>> 1. whether we also could compute MMPB(GB)SA after add Extra Points in Amber
>> Topology File?
> There have been reports of odd behavior from MMPBSA using extra points, but I
> don't know that these were ever duplicated or resolved. Maybe Ray or others
> have a better memory than I do.
>> 2. where could I download the amber version that could simulate Extra Points?
> All versions of Amber support extra points. If you find problems, please let us
> know.
> .....dac
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Mon Jan 31 2022 - 11:30:03 PST
Custom Search