Activity for APBSmem

APBSmem released /apbsmem_2.2.1.zip

APBSmem — Thu, 20 Jun 2024 17:59:02 -0000

APBSmem released /apbsmem-2.1.0.zip

APBSmem — Mon, 30 Aug 2021 22:09:02 -0000

APBSmem released /apbsmem.zip

APBSmem — Mon, 30 Aug 2021 22:02:02 -0000

APBSmem updated /README

APBSmem — Mon, 30 Aug 2021 22:00:02 -0000

Alan Lee posted a comment on discussion Help

Alan Lee — Mon, 26 Jul 2021 06:20:36 -0000

Hi, APBSmem team I'm a newbie for quantum chemistry. currently want to calculate aquos environment 's delta G for small 2D molecules(e.g generated from SMILES) to get corresponding pKa values. can it be possible to do this job by utilizing APBS calculation in JAVA？providing any examples or advice will be highly appreciated！ Regards!

APBSmem released /apbsmem-2.0.5.zip

APBSmem — Tue, 03 Mar 2020 01:32:04 -0000

Nicolas Espinoza Munoz posted a comment on discussion Help

Nicolas Espinoza Munoz — Mon, 23 Dec 2019 00:31:12 -0000

Thanks a lot guys. We'll follow your guidelines and I'll post back when we have the results. And also thanks a lot for the insight on the theory related to the charge maps. Cheers, happy holidays! Nicolás Espinoza

Frank V. Marcoline posted a comment on discussion Help

Frank V. Marcoline — Tue, 17 Dec 2019 09:15:57 -0000

Dear Nicolás Espinoza, We suggest the following two step process, which assumes linearity holds: 1) Perform a normal solvation calculation in the absence of a membrane potential. 2) Perform a calculation similar to the way apbsmem performs gating charge calculations: a) Create a copy of your protein with all of the charges set to zero. apbsmem can do this for you: java -cp /apbsmem.jar apbsmem.ChargesOff input.pqr neutral.pqr b) Perform a dummy solvation calculation with the neutral...

Nicolas Espinoza Munoz posted a comment on discussion Help

Nicolas Espinoza Munoz — Tue, 10 Dec 2019 19:51:38 -0000

Dear Mailing List users and APBSmem team, We were using APBSmem to calculate the solvation energy of a transmembrane protein, including the effect of a membrane potential. To achieve this, we took a standard pair of .in files (dummy.in and solv.in) and modified them. We set the solv.in to calculate the difference between a regular APBS vacuum state and a solvation one, with bcfl = mem and the respective conditions (memv, z_mem, etc). However, we encountered a problem when trying to scale the calculation...

Adrián García Recio posted a comment on discussion Help

Adrián García Recio — Thu, 07 Feb 2019 15:15:42 -0000

Hi Keith and Frank, first of all thank you for your fast reply and explanation. I will try to follow Frank's steps and I will give back my answer about it. Best regards, Adrián.

Frank V. Marcoline posted a comment on discussion Help

Frank V. Marcoline — Wed, 06 Feb 2019 21:23:54 -0000

Hi Adrián, You can still run APBSmem from the command line. Command line syntax: java -jar apbsmem.jar [inputfile [outputdiectory]] If you specify both the input file and output directory, the gui will still pop up, but APBSmem will run and exit when done. If the gui is an issue (for instance, if you are running on a machine without a display device) it is more complex, but still doable: 1) Run APBSmem, set up the calculation, and run it once to generate two input files: a .dummy.in file and a .solv.in...

Keith Callenberg posted a comment on discussion Help

Keith Callenberg — Wed, 06 Feb 2019 16:08:14 -0000

Hi Adrian, I do believe you can still use APBSmem 2.0.x via command line, but I defer to Frank (cc'd) who is the current maintainer. Keith On Wed, Feb 6, 2019 at 10:24 AM "Adrián García Recio" agrecio@users.sourceforge.net wrote: Hi Keith, I once used the APBSmem before (v1.3 to be more precise) via command line. I was wondering, can you still run the APBSmem 2.0 via command line? In other words, were all the improvements from v1.3 to 2.0 devoted to the GUI development?, I mean, what would be the...

Adrián García Recio posted a comment on discussion Help

Adrián García Recio — Wed, 06 Feb 2019 15:24:25 -0000

Hi Keith, I once used the APBSmem before (v1.3 to be more precise) via command line. I was wondering, can you still run the APBSmem 2.0 via command line? In other words, were all the improvements from v1.3 to 2.0 devoted to the GUI development?, I mean, what would be the best version I should use to run APBSmem via command line? Many thanks in advance! Adrián G. Recio.

APBSmem released /apbsmem-2.0.4.zip

APBSmem — Fri, 09 Nov 2018 06:35:02 -0000

APBSmem released /README

APBSmem — Fri, 09 Nov 2018 06:34:02 -0000

APBSmem released /apbsmem-2.0.3.zip

APBSmem — Fri, 11 Aug 2017 02:28:03 -0000

Keith Callenberg posted a comment on discussion Help

Keith Callenberg — Tue, 16 Aug 2016 14:08:03 -0000

Hi Krushna, Thanks for your interest in APBSmem! I am pinging Frank and Neville who...

Krushna Sonar posted a comment on discussion Help

Krushna Sonar — Tue, 16 Aug 2016 12:51:52 -0000

Hi Keith, I liked the software and kudos for the efforts in making such software....

APBSmem released /apbsmem-2.0.2.zip

APBSmem — Thu, 07 Apr 2016 19:28:03 -0000

APBSmem released /README

APBSmem — Thu, 18 Jun 2015 01:42:03 -0000

APBSmem released /apbsmem-2.0.1.zip

APBSmem — Thu, 18 Jun 2015 01:02:05 -0000

APBSmem released /apbsmem-2.0.zip

APBSmem — Tue, 27 Jan 2015 01:52:02 -0000