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No parameter for QM-link atom
#38009 08/02/20 05:27 PM
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Dear All,

I have a system of a protein with two ligands which are needed to be partitioned because it was complaining about am error 'matrix a too large"
so I added linkatoms for the resdiue in the protein and a ligand depending on the choice as follow.

ADDLinkatom QQH1 PROA 122 CB PROA 122 CA
ADDLinkatom QQH2 HETA 1 C12 HETA 1 C11
ADDLinkatom QQH3 HETA 1 C16 HETA 1 C17

In the addlink,str ,I introduced bonds, and angles for the link atom QQH2 and QQH3 ( link atoms for ligand)as follows

read rtf card append
* QM/MM link atom
*
27 2
MASS 500 QQH1 1.00800 ! Link atom for QM/MM
MASS 600 QQH2 1.00800 ! Link atom for QM/MM
MASS 700 QQH3 1.00800 ! Link atom for QM/MM

end


read param card flex append
* Parameters
*
ATOMS
MASS 500 QQH1 1.00800
MASS 600 QQH2 1.00800
MASS 700 QQH3 1.00800

! You must not have VdW parameters for the link atom

BONDS
QQH1 CN8B 0.000 1.5380
CN7 QQH1 0.000 1.5380
QQH1 CT1 0.000 1.5160
CT2 QQH1 0.000 1.5160
CT2A QQH1 0.000 1.5160
C12 QQH2 0.000 1.5160
QQH2 C11 0.000 1.5610
C16 QQH3 0.000 1.5610
QQH3 C17 0.000 1.5610

ANGLES
QQH1 CT2 CT1 0.0000 0.000
QQH1 CT2A CT1 0.0000 0.0000
QQH1 CN8B CN7 0.0000 0.000
QQH1 CN7 CN8B 0.0000 0.000
QQH2 C12 C11 0.000 0.000
QQH3 C16 C17 0.000 0.000


But when running the inp file following warning was shown eventhough the linkatoms were located.

ADDLinkatom QQH2 HETA 1 C12 HETA 1 C11

Message from MAPIC: Atom numbers are changed.

***** LEVEL 0 WARNING FROM *****
***** No parameter for QM-link atom
******************************************
BOMLEV ( -1) IS NOT REACHED. WRNLEV IS 5

ADDLNAT: Link atom placed 1.00000 A from QM atom.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 4 Number of residues = 6544
Number of atoms = 27412 Number of groups = 8840
Number of bonds = 27529 Number of angles = 23586
Number of dihedrals = 25869 Number of impropers = 1603
Number of cross-terms = 608
Number of HB acceptors = 6801 Number of HB donors = 12877
Number of NB exclusions = 0 Total charge = 6.00000

CHARMM> ADDLinkatom QQH3 HETA 1 C16 HETA 1 C17

Message from MAPIC: Atom numbers are changed.

***** LEVEL 0 WARNING FROM *****
***** No parameter for QM-link atom
******************************************
BOMLEV ( -1) IS NOT REACHED. WRNLEV IS 5

ADDLNAT: Link atom placed 1.00000 A from QM atom.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 4 Number of residues = 6544
Number of atoms = 27413 Number of groups = 8841
Number of bonds = 27531 Number of angles = 23587
Number of dihedrals = 25869 Number of impropers = 1603
Number of cross-terms = 608
Number of HB acceptors = 6801 Number of HB donors = 12877
Number of NB exclusions = 0 Total charge = 6.00000

There is no any specific solution when I searched throughout the forum and I guess it is not something I can ignore.
So does anyone has a solution for this ? did I make a mistake somewhere else?
I would appreciate if you can give me hand on this.

Thanks

Re: No parameter for QM-link atom
vht #38013 08/04/20 11:05 AM
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The error message is just telling you that the link atom doesn't initially exist. The next two messages tell you it's been created and the PSF modified:

Code
ADDLNAT: Link atom placed 1.00000 A from QM atom.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.

You can make CHARMM spit out a PDB if you want to check. e.g.

Code
open write unit 10 card name my_linkAtom_check.pdb
write coor unit 10 pdb

Re: No parameter for QM-link atom
vht #38014 08/04/20 06:32 PM
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or using the modern (since 25 years or so), simpler and less error prone I/O construct:

write coor pdb name my_linkAtom_check.pdb
* and don't forget the title...
*


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: No parameter for QM-link atom
vht #38015 08/05/20 06:23 AM
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vht Offline OP
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Thanks you very much.I appreciate your help on this.


Moderated by  BRBrooks, lennart, rmv 

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