Dear all,
Following molecule (methyl phosphate)
gives a bond assignment problem in antechamber (amber8)
although I have the impression that charges are calculated correctly.
(see input & output files below)
Other molecules (without Phosphate) worked fine.
I have no idea where the problem is.
Best regards,
matheus froeyen
---------------------------------------------
dommelsch 408% $AMBERHOME/exe/antechamber
-i test.pdb -fi pdb -o test.mol2 -fo mol2 -nc -2 -c bcc
Cannot successfully assign bond type for this molecule, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
Total number of electrons: 58; net charge: -2
Running: /d2/sw/amber/amber8/exe/divcon
Cannot successfully assign bond type for this molecule, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
dommelsch 410% $AMBERHOME/exe/parmchk -i test.mol2 -f mol2 -o frcmod
dommelsch 411% cat test.pdb
COMPND Title
REMARK 1 PDB to MMOD atom-numbering translation table; the mmod
numbers
REMARK 1 pertain to the .dat file from which this file was created,
REMARK 1 not to one created from this file:
REMARK 1 PDB: 1 2 3 4 5 6 7 8 9
REMARK 1 MMOD: 1 2 3 4 5 6 7 8 9 /
HETATM 1 P01 UNK 0 11.194 8.941 0.031 0.75 0.75 0
HETATM 2 O02 UNK 0 12.415 9.970 -0.217 -0.33 -0.33 0
HETATM 3 OM3 UNK 0 11.325 7.945 -1.160 -0.80 -0.80 0
HETATM 4 OM4 UNK 0 11.516 8.336 1.431 -0.80 -0.80 0
HETATM 5 O05 UNK 0 9.936 9.859 -0.015 -0.80 -0.80 0
HETATM 6 C06 UNK 0 12.657 11.064 0.671 -0.13 -0.13 0
HETATM 7 H07 UNK 0 13.521 11.627 0.319 0.04 0.04 0
HETATM 8 H08 UNK 0 11.784 11.717 0.695 0.04 0.04 0
HETATM 9 H09 UNK 0 12.854 10.685 1.674 0.04 0.04 0
CONECT 1 2 3 4
CONECT 1 5
CONECT 1 5
CONECT 2 1 6
CONECT 3 1
CONECT 4 1
CONECT 5 1
CONECT 5 1
CONECT 6 2 7 8 9
CONECT 7 6
CONECT 8 6
CONECT 9 6
END
dommelsch 412% cat test.mol2
.<TRIPOS>MOLECULE
UNK
9 8 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 P01 11.1940 8.9410 0.0310 p5 1 UNK
1.4978
2 O02 12.4150 9.9700 -0.2170 os 1 UNK
-0.5731
3 OM3 11.3250 7.9450 -1.1600 o 1 UNK
-0.9802
4 OM4 11.5160 8.3360 1.4310 o 1 UNK
-0.9939
5 O05 9.9360 9.8590 -0.0150 o 1 UNK
-1.0318
6 C06 12.6570 11.0640 0.6710 c3 1 UNK
0.2092
7 H07 13.5210 11.6270 0.3190 h1 1 UNK
-0.0892
8 H08 11.7840 11.7170 0.6950 h1 1 UNK
-0.0209
9 H09 12.8540 10.6850 1.6740 h1 1 UNK
-0.0178
.<TRIPOS>BOND
1 1 2 1
2 1 3 2
3 1 4 2
4 1 5 1
5 2 6 1
6 6 7 1
7 6 8 1
8 6 9 1
.<TRIPOS>SUBSTRUCTURE
1 UNK 1 TEMP 0 **** **** 0 ROOT
dommelsch 417% cat frcmod
remark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
NONBON
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Received on Wed Jun 09 2004 - 08:53:00 PDT
