VMD-L Mailing List

From: Cindy Cregier (cindy.cregier_at_REMOVE_yahoo.com)
Date: Wed Jul 05 2023 - 01:14:37 CDT

When creating a water box using VMD, would it be valid to edit the wat.top file to conform to CHARMM36 specifications?  
The wat.top file sent with the updates is as follows:
27  1

MASS  4 HT   1.00800 H ! TIPS3P WATER HYDROGENMASS 75 OT  15.99940 O ! TIPS3P WATER OXYGEN
RESI TIP3   0.000 ! tip3p water model, generate using noangle nodihedralGROUPATOM OH2  OT  -0.834ATOM H1   HT   0.417ATOM H2   HT   0.417!BOND OH2 H1 OH2 H2 H1 H2    ! the last bond is needed for shakeBOND OH2 H1 OH2 H2ANGLE H1 OH2 H2     ! requiredACCEPTOR OH2PATCHING FIRS NONE LAST NONE
END

I'd like to edit the wat.top file so that the line with the H-H "bond" is uncommented, and the version is changed to 31:

31  1
MASS  -1  HT         1.00800 H ! TIPS3P WATER HYDROGENMASS  -1  OT        15.99940 O ! TIPS3P WATER OXYGEN

RESI TIP3         0.000 NOANG NODIH ! tip3p water modelGROUPATOM OH2  OT     -0.834ATOM H1   HT      0.417ATOM H2   HT      0.417BOND OH2 H1 OH2 H2 H1 H2    ! the last bond is needed for shakeANGLE H1 OH2 H2             ! requiredDONOR H1 OH2DONOR H2 OH2ACCEPTOR OH2PATCHING FIRS NONE LAST NONE
END
Along the same vein, would the wat.psf file used by solvate.tcl work, or would a similar file need to be created using the CHARMM36 specifications for water?  What specifications were used to make the wat.psf file used by VMD? 
I appreciate any insight you may have!Cindy