Hello,
u wish to create the parameters file, i.e., prepin file then why r u creating
mol2 file. u hav pdb then use it directly in following command:
$AMBERHOME/exe/antechamber -i ____.pdb -fi db -o ___.prepin -fo prepi -c bcc -s 2
n why r u adding hydrogens to this pdb. i didn't find it in the tutorial(
tutorial 5) n even if ur adding then what is "new" there as in
HETATM 0 H5'2 LLP B 51 -16.889 -3.838 31.149 1.00 22.01 H new
HETATM 0 H5'1 LLP B 51 -17.298 -5.346 31.978 1.00 22.01 H new
HETATM 0 H4'2 LLP B 51 -17.467 -7.530 29.837 1.00 23.40 H new
i think either u should not add hydrogen or even if ur adding then u should add
TER card after each one instead of "new" keyword. This error usually comes when
there is
some problem with the pdb. However, i don't know exactly and i might be wrong so
excuse me for if i hav written anythng wrong, but u may try it out. Wish u good
luck.
with regards,
Nicee.
> hi all
> i want to extract parameters for pyridoxal phosphate molecule through antechamber
> i got the pdb and then reduce it i.e. added hydrogens as per the instructions
given in tutorial
> but then i gave following command:
> antechamber -i plp_h_try.pdb -fi pdb -o plp_h_try.mol2 -fo mol2 -c bcc -s 2
>
> i got following files:
> ANTECHAMBER_BOND_TYPE.AC
> ATOMTYPE.INF
> ANTECHAMBER_BOND_TYPE.AC0
> and gave following error:
> Running: /home/username/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac -j full
>
> Warning: the assigned bond types may be wrong, 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
> (4) increase PSCUTOFF in define.h and recompile bondtype.C
> Be cautious, use a large value of PSCUTOFF (>10) will significantly
increase
> the computer time
> Error: cannot run "/home/username/amber9/exe/bondtype -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in
judgebondtype() of antechamber.c properly, exit
>
> it is not giving me the final result file as given in the tutorial i.e.
ANTECHAMBER_AC.AC ANTECHAMBER_AM1BCC_PRE.AC ATOMTYPE.INF mopac.out
sustiva.mol2
> ANTECHAMBER_AC.AC0 ANTECHAMBER_BOND_TYPE.AC divcon.pdb mopac.pdb
sustiva.pdb
> ANTECHAMBER_AM1BCC.AC ANTECHAMBER_BOND_TYPE.AC mopac.in
>
> can anyone plz help me out to solve this problem
>
> thanx
> monica
>
> my pdb input is like:
> USER MOD reduce.3.13.080428 H: found=0, std=0, add=20, rem=0, adj=0 HETATM
2763 N1 LLP B 51 -20.316 -3.740 29.288 1.00 21.66 N HETATM
2764 C2 LLP B 51 -20.961 -4.935 28.990 1.00 22.87 C HETATM
2765 C2' LLP B 51 -22.294 -4.941 28.286 1.00 22.04 C HETATM
2766 C3 LLP B 51 -20.362 -6.157 29.325 1.00 23.02 C HETATM
2767 O3 LLP B 51 -20.985 -7.190 29.030 1.00 24.43 O HETATM
2768 C4 LLP B 51 -19.110 -6.166 29.990 1.00 23.70 C HETATM
2769 C4' LLP B 51 -18.395 -7.425 30.418 1.00 23.40 C HETATM
2770 C5 LLP B 51 -18.476 -4.924 30.279 1.00 23.30 C HETATM
2771 C6 LLP B 51 -19.093 -3.730 29.931 1.00 21.46 C HETATM
2772 C5' LLP B 51 -17.155 -4.893 30.986 1.00 22.01 C HETATM
2773 OP4 LLP B 51 -16.014 -5.543 30.366 1.00 21.12 O HETATM
2774 P LLP B 51 -14.844 -6.236 31.204 1.00 22.72 P HETATM
2775 OP1 LLP B 51 -15.564 -7.291 31.925 1.00 24.68 O HETATM
2776 OP2 LLP B 51 -13.868 -6.668 30.208 1.00 22.94 O HETATM
2777 OP3 LLP B 51 -14.290 -5.162 32.077 1.00 21.46 O HETATM
2778 N LLP B 51 -18.530 -10.222 25.325 1.00 23.17 N HETATM
2779 CA LLP B 51 -18.180 -11.436 26.091 1.00 22.92 C HETATM
2780 CB LLP B 51 -19.231 -11.722 27.143 1.00 22.80 C HETATM
2781 CG LLP B 51 -19.386 -10.657 28.201 1.00 22.54 C HETATM
2782 CD LLP B 51 -18.088 -10.432 28.969 1.00 24.97 C HETATM
2783 CE LLP B 51 -18.317 -9.796 30.349 1.00 26.35 C HETATM
2784 NZ LLP B 51 -19.140 -8.522 30.259 1.00 28.13 N HETATM
2785 C LLP B 51 -17.952 -12.686 25.216 1.00 22.89 C HETATM
2786 O LLP B 51 -17.351 -13.679 25.654 1.00 21.99 O HETATM
0 H5'2 LLP B 51 -16.889 -3.838 31.149 1.00 22.01 H new
> HETATM 0 H5'1 LLP B 51 -17.298 -5.346 31.978 1.00 22.01 H
new
> HETATM 0 H4'2 LLP B 51 -17.467 -7.530 29.837 1.00 23.40 H
new
> HETATM 0 H4'1 LLP B 51 -18.104 -7.335 31.475 1.00 23.40 H
new
> HETATM 0 H2'3 LLP B 51 -23.032 -4.396 28.893 1.00 22.04 H
new
> HETATM 0 H2'2 LLP B 51 -22.194 -4.453 27.305 1.00 22.04 H
new
> HETATM 0 H2'1 LLP B 51 -22.630 -5.979 28.145 1.00 22.04 H
new
> HETATM 0 HZ1 LLP B 51 -20.127 -8.507 30.099 1.00 28.13 H
new
> HETATM 0 HN2 LLP B 51 -17.930 -9.903 24.592 1.00 23.17 H
new
> HETATM 0 HG3 LLP B 51 -19.702 -9.715 27.730 1.00 22.54 H
new
> HETATM 0 HG2 LLP B 51 -20.182 -10.949 28.902 1.00 22.54 H
new
> HETATM 0 HE3 LLP B 51 -18.829 -10.517 31.004 1.00 26.35 H
new
> HETATM 0 HE2 LLP B 51 -17.346 -9.572 30.814 1.00 26.35 H
new
> HETATM 0 HD3 LLP B 51 -17.570 -11.394 29.095 1.00 24.97 H
new
> HETATM 0 HD2 LLP B 51 -17.424 -9.784 28.377 1.00 24.97 H
new
> HETATM 0 HB3 LLP B 51 -20.200 -11.862 26.642 1.00 22.80 H
new
> HETATM 0 HB2 LLP B 51 -18.984 -12.673 27.637 1.00 22.80 H
new
> HETATM 0 HA LLP B 51 -17.215 -11.217 26.572 1.00 22.92 H
new
> HETATM 0 H6 LLP B 51 -18.606 -2.772 30.168 1.00 21.46 H
new
> HETATM 0 H LLP B 51 -19.367 -9.719 25.540 1.00 23.17 H
new
> TER
> END
>
>
>
>
>
>
>
>
>
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Received on Tue Jun 15 2010 - 04:30:04 PDT
