VMD-L Mailing List

From: Reinke.Patrick_at_mh-hannover.de
Date: Sat Dec 21 2019 - 12:26:37 CST

Hello VMD user,

I ran a MD simulation with my native protein without any problems (prepared with VMD auto psf builder + solvate + autoionize). Then I added a phosphoserine via patch (SP2-patch with VMD auto psf Builder). The phosphate was visible after Auto PSF builder, so I executed the VMD "add solvate box". I observed that the waterbox was generated, but it was not size minimized. Subsequent Autoionizing with VMD was not successful, the net charge was wrong (see error messages below).

Do I need to neutralize the patches separately?
I got the SP2-toppar parameter files from mackerell.umaryland.edu.

Greetings Patrick

Error popup:
System had a non-integer total charge. There was likely a problem in the process of building it.

error in TKconsole:
psfgen) NBFix between carboxylate and sodium
psfgen)
psfgen) skipping statements at end of file due to end or return statement
psfgen) building segment ION
psfgen) setting patch for first residue to NONE
psfgen) setting patch for last residue to NONE
psfgen) Info: generating structure...segment complete.
Autoionize) Randomizing ion positions...
Autoionize) Assigning ion coordinates...
psfgen) Info: writing psf file aaionized3.psf
psfgen) total of 507480 atoms
psfgen) total of 340065 bonds
psfgen) total of 177030 angles
psfgen) total of 14045 dihedrals
psfgen) total of 938 impropers
psfgen) total of 0 explicit exclusions
psfgen) total of 318 cross-terms
psfgen) Info: psf file complete.
psfgen) Info: writing pdb file aaionized3.pdb
psfgen) Info: pdb file complete.
Autoionize) Loading new system with added ions...
Autoionize) System net charge after adding ions: -0.08999377489089966e.
Autoionize) All done. 

--
Patrick Reinke
Medizinische Hochschule Hannover
Institut für Biophysikalische Chemie
OE4350,Carl-Neuberg-Str. 1, D-30625 Hannover
Tel.: +49(0)511-532-5177
reinke.patrick_at_mh-hannover.de
www.mh-hannover.de