AMBER Archive (2004)

Subject: Re: AMBER: antechamber

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Wed Jun 09 2004 - 09:05:02 CDT

Hi,

If you use -j 5 with antechamber, those bond type assignment message may
disappear. But if you compare the output created with and without -j 5,
they may look the same. This is just based on my experience.

Guanglei

Matheus Froeyen wrote:
> 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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