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#36570 - 08/18/17 08:45 AM patch residue problem
madape Offline
Forum Member

Registered: 08/13/17
Posts: 2
Dear all,

I got a simple but tricky question: Simulation metalloprotein.

After been reading in the forum possibilities to ensure zinc coordination:

1. Rely on ELEC and VDW, indeed stone parameters for zinc ion. This option does not work properly for me, some coordination bonds are lost.

2. I launch QM/MM calculations, but its too expensive.

Therefore I decided to choose two options:

Add NOE restraints or Patch residue.

My question comes from this last because I am not sure how to implemented and I got an error. My files look like:

* Append the PDBs

! Read topology and parameter files
stream toppar.str

! Read PSF and coordinates from file
read psf card name step1_pdbreader.psf
read coor card name step1_pdbreader.crd

patch ZNSP HETA 62 PROA 50 PROA 57 PROA 59 PROA 60 setup warn
autogen angle dihe

coor init sele hydrogen end

write psf card name final.psf
write coor card name final.crd

and my output:

Warning from PSFSUM: The sum of charges ( -4.280000) is not an integer

***** LEVEL 0 WARNING FROM *****
***** Total charge not an integer

Please, can anyone help me? Because I cannot keep no it
Thank you in advance

toppar_all22_cys.txt (350 downloads)

#36571 - 08/18/17 11:05 AM Re: patch residue problem [Re: madape]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8079
Loc: 39 03 48 N, 77 06 54 W
The warning means that applying the patch results in a non-integer charge for the molecule; you need to take the charges of the deleted hydrogens into account.
Rick Venable
computational chemist

#36574 - 08/30/17 02:09 AM Re: patch residue problem [Re: madape]
madape Offline
Forum Member

Registered: 08/13/17
Posts: 2
Okay, thank you Rick.


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