CpHMD: Warning when building atom of unknown mass (psfgen)

From: Aalap Parikh (aalap.parikh_at_ucalgary.ca)
Date: Tue Jun 30 2020 - 15:35:37 CDT

Hello,

I had a question about a particular warning message I have encountered during my usage of the CpHMD implementation in NAMD.

The warning message appears when the initial dummy atom patches are applied at the beginning of the CpHMD run. These patches are defined in a CpHMD specific topology file (top_cph36_prot.rtf) which is distinct from the topology and parameters of the starting structure and are used to define the various possible protonation states of titratable residues. The dummy hydrogen mass is defined in the CpHMD specific parameter file (par_cph36_prot.prm) with the line:
“MASS 131 HD 1.00800 ! polar H dummy”

I am wondering why the WARNING! Message (shown in the psfgen excerpt below from the log file) is given. Specifically, why is the program seemingly unable to recognize the mass of the dummy atom, which is already defined in the parameter file? In what scenarios other than mass repartitioning might this warning lead to errors? How is the unknown mass ultimately assigned? I did not find much about this particular warning after a web search.

TCL: namdcph) initializing constant pH PSF...
psfgen) clearing structure, preserving topology and aliases
psfgen) reading structure from psf file ../topology/ace_asp_nme.psf
psfgen) reading coordinates, insertion codes, and element symbols from pdb file ../topology/ace_asp_nme.pdb
psfgen) reading coordinates from namdbin file ../topology/ace_asp_nme.coor
psfgen) reading velocities from velnamdbin file ../topology/ace_asp_nme.vel
psfgen) applying patch ASPD to 1 residue(s)
PROT:1
TCL: WARNING! Building new atom PROT:1:HD1 with unknown mass.
TCL: This may cause issues, for example, with mass repartitioning.
TCL: WARNING! Building new atom PROT:1:HD2 with unknown mass.
TCL: This may cause issues, for example, with mass repartitioning.
psfgen) Info: guessing coordinates for 2 atoms (0 non-hydrogen)
TCL: cphpsfgen) creating new alchemical side chain for PROT:1:ASP
psfgen) applying patch ASPH1 to 1 residue(s)
PROT:1
TCL: cphpsfgen) merging alchemical sidechains for PROT:1:ASP
psfgen) regenerating all angles
psfgen) regenerating all dihedrals

Also, when I restart the CpHMD simulation using the generated PSF (which now contains the dummy atoms), no warning is given:

TCL: namdcph) initializing constant pH PSF...
psfgen) clearing structure, preserving topology and aliases
psfgen) reading structure from psf file 4.1/ace_asp_nme_prod0.psf
psfgen) reading coordinates, insertion codes, and element symbols from pdb file 4.1/ace_asp_nme_prod0.pdb
psfgen) reading coordinates from namdbin file 4.1/ace_asp_nme_prod0.coor
psfgen) reading velocities from velnamdbin file 4.1/ace_asp_nme_prod0.vel
psfgen) duplicate topology file ../../toppar/top_cph36_prot.rtf
psfgen) applying patch ASPD to 1 residue(s)
PROT:1
psfgen) Info: guessing coordinates for 0 atoms (0 non-hydrogen)
TCL: cphpsfgen) creating new alchemical side chain for PROT:1:ASP
psfgen) applying patch ASPH1 to 1 residue(s)
PROT:1
TCL: cphpsfgen) merging alchemical sidechains for PROT:1:ASP
psfgen) regenerating all angles
psfgen) regenerating all dihedrals

Thanks for the assistance,
Aalap

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