- I’d like to have fort.38 in step 4 and sum_crg.out; pK.out etc in step 5 alrady have it in step 4, script to do it again
- The corrected sum_crg (using head3.lst for charge)
- the mfe analysis in pK.out (and an ability to change the mfe point from pK to a pH by retuning step 5 mfe.py
- Change in chemical potential of a ligand chosen in run.prm, temp fix script, automated
- Bug, step1 can not handle NTR and CTR correctly when the NTR and CTR atoms are out of order.
- The program stops and returns an error message From users' feedback
- more than the maximum number of conformers Why the error happens and not printed out clearly
- the number of conformers in all input files (head3.lst; opp etc) don’t match Check the consistency
- write out for Asp, Glu, Arg, Lys: which ones are <90% ionized and the total number (if you have a lot of neutral Arg the run is likely to be bad) A tool or step 4, print out abnoramlies, chi2, n etc
- Do not pass 0 radius H to delphi to see if this fixes delphi surface error. Implement in the next version
- Fix delphi run time error.
- Strip down and reorganize run.prm;
- have full.prm (with all possibilities) on Wiki. Good idea, group options that default to a pre-defined choices
- One run.prm with a toggle for run quick or default (rather than 2 different basic input files) Questionaire for determining the run.prm
- Proton naming;
- new tpl files, take both tpl, ftpl
- Python scripts to show titration; doable
- Phi Map instructions Ask Dyvia? On a single delphi input file from microstate, or most occupied confomer structure