[gmx-users] Both atom and residue type four letters . . .

[Marc Charendoff]

Hello,
 
Well, I have tried a couple of permuatations and I seem to clear up one problem only to get another. Any hints as to what to do when both atomtype AND residuetype each are four letter designates? Not seeing anything in the manual.
 
Thanks again.
 
 
Back Off! I just backed up posre_A.itp to ./#posre_A.itp.6#
Processing chain 2 'B' (2 atoms, 2 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../src/kernel/pdb2gmx.c, line: 421
Fatal error:
Atom ZN2+ in residue ZN2+ 1 not found in rtp entry with 1 atoms
while sorting atoms
-------------------------------------------------------
"Kick the Dog and You Will Die" (Magnapop)PDB (only atom type -1) . . . 
 
ATOM 1913 CD1 ILE A 240 22.075 30.322 -3.413 1.00 16.47 .000
ATOM 1914 ZN2+ ZN2+ A 241 11.832 23.652 11.052 1.00 20.05 .000
ATOM 1915 ZN2+ ZN2+ A 242 11.551 25.149 14.101 1.00 23.28 .000
ATOM 1916 O HOH A 243 11.793 23.332 13.260 1.00 19.06 .000
ATOM 1917 HW1 HOH A 243 12.609 23.332 13.837 1.00 0.00
ATOM 1918 HW2 HOH A 243 10.977 23.332 13.837 1.00 0.00
 OR the other way . . .
 
Back Off! I just backed up trp.top to ./#trp.top.9#
Processing chain 1 'A' (1915 atoms, 242 residues)
There are 346 donors and 363 acceptors
There are 546 hydrogen bonds
Will use HISB for residue 20
Will use HISA for residue 94
Will use HISB for residue 96
Will use HISA for residue 99
Will use HISB for residue 123
Will use HISB for residue 135
Will use HISA for residue 159
Will use HISA for residue 163
Will use HISA for residue 225
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../src/kernel/resall.c, line: 436
Fatal error:
Residue 'N2+' not found in residue topology database
-------------------------------------------------------
"Here's the Way It Might End" (G. Michael)
 Alternate PDB ( atom ANDresidue types -1) 
 
ATOM 1913 CD1 ILE A 240 22.075 30.322 -3.413 1.00 16.47 .000
ATOM 1914 ZN2+ZN2+ A 241 11.832 23.652 11.052 1.00 20.05 .000
ATOM 1915 ZN2+ZN2+ A 242 11.551 25.149 14.101 1.00 23.28 .000
ATOM 1916 O HOH A 243 11.793 23.332 13.260 1.00 19.06 .000
ATOM 1917 HW1 HOH A 243 12.609 23.332 13.837 1.00 0.00
ATOM 1918 HW2 HOH A 243 10.977 23.332 13.837 1.00 0.00
END. . .
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