Activity for APBSmem
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APBSmem released /apbsmem_2.2.1.zip
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Alan Lee posted a comment on discussion Help
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!
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Nicolas Espinoza Munoz posted a comment on discussion Help
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
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Frank V. Marcoline posted a comment on discussion Help
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 <path_to_apbsmem>/apbsmem.jar apbsmem.ChargesOff input.pqr neutral.pqr b) Perform a dummy solvation calculation with the neutral...
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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...
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Adrián García Recio posted a comment on discussion Help
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.
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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...
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Keith Callenberg posted a comment on discussion Help
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...
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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.
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Hi Krushna, Thanks for your interest in APBSmem! I am pinging Frank and Neville who...
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Krushna Sonar posted a comment on discussion Help
Hi Keith, I liked the software and kudos for the efforts in making such software....
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