Hi Case,
Thank you for your reply. I checked Note 6 at p.88 of my Amber User's
Guide, about AM1 Mulliken charges taht are required for the AM1-BCC
procedure...etc. (I suppose it is what you hope me to check first). I
tried to use acdoctor to analyze my ligand pdb file before changing
values of namelist of sqm, I found something very intersting. acdoctor
told me that it could not detect hydrogens in the ligand, but I
already added hydrogens to the ligand. Besides, acdoctor seemed not to
run successfully. Now I suspect if the major problem probably is from
my ligand's pdb file, even if I cannot perceive problems on Chimera
and AutodockTool. Could you help me to find out the potential problems
of ligands' pdb (showed below after the informatio of acdoctor.) Thank
you and other people for your kindly suggestions so far.
Sincerely,
Crystal
=================message printed out by acdoctor=================
[crystal.pdb-p690-2 ligand]$ acdoctor -i TPP_MD1.2.pdb -fi pdb
-- Check Unusual Elements --
-- Status: pass --
-- Check Open Valences --
Warning: There are no hydrogen and halogens in this molecule, it is
highly possible that this molecule has open valence
-- Check Geometry --
-- For those bonded --
-- For those unbonded --
-- Status: pass --
-- check weird bonds --
-- Status: pass --
-- Check if the input is only one unit --
-- Status: pass --
-- Now try to judge bond type --
-- Now try to assign atom type --
Running: /home/crystal/amber11/bin/atomtype -i ACDOCTOR_BOND.ac -o
ACDOCTOR_ATOM.ac -p gaff
Cannot open the ac input file: ACDOCTOR_BOND.ac, exit
Error: cannot run "/home/crystal/amber11/bin/atomtype -i
ACDOCTOR_BOND.ac -o ACDOCTOR_ATOM.ac -p gaff" in main() of
antechamber.c properly, exit
=================pdb of my ligand=================================
HETATM 1 CM2 TPS A 97 17.418 39.613 64.156 1.00 58.49 C
HETATM 2 N3 TPS A 97 23.243 40.700 66.912 1.00 67.59 N
HETATM 3 C2 TPS A 97 23.199 39.970 68.047 1.00 71.06 C
HETATM 4 S1 TPS A 97 24.466 38.888 68.263 1.00 76.57 S
HETATM 5 C5 TPS A 97 25.169 39.393 66.749 1.00 70.29 C
HETATM 6 C4 TPS A 97 24.377 40.358 66.173 1.00 68.02 C
HETATM 7 CM4 TPS A 97 24.654 41.037 64.864 1.00 66.37 C
HETATM 8 C6 TPS A 97 26.442 38.827 66.231 1.00 71.69 C
HETATM 9 C7 TPS A 97 27.616 39.541 66.788 1.00 73.89 C
HETATM 10 O7 TPS A 97 28.905 39.096 66.364 1.00 79.36 O
HETATM 11 N1A TPS A 97 19.565 39.335 65.174 1.00 60.93 N
HETATM 12 C2A TPS A 97 18.621 40.228 64.715 1.00 60.35 C
HETATM 13 N3A TPS A 97 18.771 41.525 64.751 1.00 60.24 N
HETATM 14 C4A TPS A 97 19.928 42.077 65.291 1.00 62.58 C
HETATM 15 N4A TPS A 97 20.071 43.399 65.302 1.00 64.99 N
HETATM 16 C5A TPS A 97 20.949 41.195 65.832 1.00 61.43 C
HETATM 17 C6A TPS A 97 20.705 39.842 65.708 1.00 59.88 C
HETATM 18 C7A TPS A 97 22.173 41.745 66.539 1.00 63.99 C
HETATM 19 P1 TPS A 97 30.294 39.595 66.914 1.00 82.55 P
HETATM 20 O1 TPS A 97 30.380 41.061 66.691 1.00 85.74 O
HETATM 21 O2 TPS A 97 31.266 38.801 66.119 1.00 82.04 O
HETATM 22 O3 TPS A 97 30.331 39.285 68.379 1.00 79.73 O
HETATM 23 HM21 TPS A 97 16.733 40.392 63.821 1.00 0.00 H
HETATM 24 HM22 TPS A 97 16.932 39.006 64.920 1.00 0.00 H
HETATM 25 HM23 TPS A 97 17.692 38.982 63.311 1.00 0.00 H
HETATM 26 H2 TPS A 97 22.402 40.075 68.768 1.00 0.00 H
HETATM 27 HM41 TPS A 97 25.576 40.642 64.437 1.00 0.00 H
HETATM 28 HM42 TPS A 97 24.760 42.110 65.027 1.00 0.00 H
HETATM 29 HM43 TPS A 97 23.828 40.853 64.177 1.00 0.00 H
HETATM 30 H62 TPS A 97 26.502 37.775 66.509 1.00 0.00 H
HETATM 31 H63 TPS A 97 26.455 38.911 65.144 1.00 0.00 H
HETATM 32 H72 TPS A 97 27.523 40.591 66.512 1.00 0.00 H
HETATM 33 H73 TPS A 97 27.573 39.470 67.875 1.00 0.00 H
HETATM 34 H4A1 TPS A 97 20.905 43.813 65.692 1.00 0.00 H
HETATM 35 H4A2 TPS A 97 19.345 43.989 64.920 1.00 0.00 H
HETATM 36 H6A TPS A 97 21.460 39.151 66.054 1.00 0.00 H
HETATM 37 H7A2 TPS A 97 22.637 42.483 65.884 1.00 0.00 H
HETATM 38 H7A3 TPS A 97 21.849 42.247 67.450 1.00 0.00 H
CONECT 3 26 4 2
CONECT 12 13 11 1
CONECT 6 7 5 2
CONECT 14 16 15 13
CONECT 5 8 6 4
CONECT 16 18 17 14
CONECT 8 31 30 9 5
CONECT 17 36 16 11
CONECT 9 33 32 10 8
CONECT 18 38 37 16 2
CONECT 1 25 24 23 12
CONECT 7 29 28 27 6
CONECT 26 3
CONECT 34 15
CONECT 35 15
CONECT 30 8
CONECT 31 8
CONECT 36 17
CONECT 32 9
CONECT 33 9
CONECT 37 18
CONECT 38 18
CONECT 23 1
CONECT 24 1
CONECT 25 1
CONECT 27 7
CONECT 28 7
CONECT 29 7
CONECT 11 17 12
CONECT 2 18 6 3
CONECT 13 14 12
CONECT 15 35 34 14
CONECT 20 19
CONECT 21 19
CONECT 22 19
CONECT 10 9 19
CONECT 19 22 21 20 10
CONECT 4 3 5
END
On 11/14/11, case <case.biomaps.rutgers.edu> wrote:
> On Mon, Nov 14, 2011, Crystal.CHIA-YU Ku wrote:
>
>> QMMM: ERROR!
>> QMMM: Unable to achieve self consistency to the tolerances specified
>> QMMM: No convergence in SCF after 1000 steps.
>> QMMM: E = -0.6139E+06 DeltaE = 0.1467E-10 DeltaP = 0.1322E-07
>> QMMM: Smallest DeltaE = 0.1023E-11 DeltaP = 0.7705E-07 Step = 853
>
> Looks like it got close. Please see Note 6 on p.88 of the AmberTools Users'
> Manual.
>
> ...good luck...dac
>
>
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>
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Received on Mon Nov 14 2011 - 17:00:03 PST
