Poisson operator

[1ESl]

Hello While running APBS I want to obtain map of Poisson operator. When i run the program, it writes on the screen: Writing Poisson operator matrix to poissom_21.9.mat..., but file can not be found. We also tried on a DNA tutorial input file and the same thing happen. Could you tell me if there is a bug in the code, or is it suppose to work normally and I have a mistake in an input file. Please find my input file in attachment. run_spacing0.1786.pdf

[sobolevnrm]

The PDF didn't work for me; here are the contents of the input file from the original email:

read
    mol pqr vaja_centerzz.pqr
    kappa dx kappa_16.9_spac0.17.dx 
    diel dx dielx_15.9_spac0.17.dx diely_15.9_spac0.17.dx dielz_15.9_spac0.17.dx
end
elec name polar
    mg-auto
    dime 353 353 225
    cglen 63 63 40
    fglen 63 63 40
    cgcent mol 1
    fgcent mol 1
    mol 1
    srfm mol
    srad 0.0
    npbe 
    bcfl zero 
    pdie 1.0 #2
    sdie 75.5 #75.5
    ion charge 1.0 conc 0.15 radius 2
    ion charge -1.0 conc 0.15 radius 2
    chgm spl2 
    sdens 10.00 
    swin 0.30 
    temp 298.15
    calcenergy total 
    calcforce no
    #write pot dx pot_0.1786_16.9
    #write charge dx charge_0.1786_16.9
    writemat poisson poissom_21.9 
    usemap diel 1
    usemap kappa 1
end
quit

[sobolevnrm]

@intendo and @ashermancinelli - who is the write person to work on this?

[ashermancinelli]

I'd like to get more familiar with the interface so you may assign to me if you like.

@intendo if you're confident in your understanding of this problem and would like to take it, I'd appreciate being looped in!

[ashermancinelli]

@1ESl with what options did you build and invoke apbs? I can't seem to open the pdf attachment you sent.

[1ESl]

Hi. We build it from source code from sourceforge. We try different input files, but the writemap function did not work. While running APBS, it is written in terminal that map is written, but file can not be found. Please find my input file in attachment.

V V pon., 5. okt. 2020 ob 23:09 je oseba Asher Mancinelli < notifications@github.com> napisala:

@1ESl https://github.com/1ESl with what options did you build and invoke apbs? I can't seem to open the pdf attachment you sent.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Electrostatics/apbs/issues/87#issuecomment-703890411, or unsubscribe https://github.com/notifications/unsubscribe-auth/AREJMTZ2GP2VQLLPSJYYHALSJIY2BANCNFSM4RZGFD7A .

[ashermancinelli]

@1ESl Would you upload the file to this issue on github? Thank you in advance.

@intendo @sobolevnrm Do either of you know if we have a branch/tag for the source release on SF? The commit hash on SF is 7ae0c0, and I can't find that hash in any branch history.

[intendo]

The v3.0.0 tagged release on SF is actually from https://github.com/Electrostatics/apbs-pdb2pqr.git. The repo was split up into apbs and pdb2pqr and the only version I can get to work from there is branch darren/valgrind.

[ashermancinelli]

In that case, @1ESl could you retry your example with this repo instead of the SF mirror?

[1ESl]

Yes. I will try and see if that works for writemap.

V V tor., 6. okt. 2020 ob 22:24 je oseba Asher Mancinelli < notifications@github.com> napisala:

In that case, @1ESl https://github.com/1ESl could you retry your example with this repo instead of the SF mirror?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Electrostatics/apbs/issues/87#issuecomment-704532571, or unsubscribe https://github.com/notifications/unsubscribe-auth/AREJMTYHKQRVN3MOUBH4VOLSJN4IZANCNFSM4RZGFD7A .