Hi Case,
Here is the content of my sqm.out file: ( I rip the information may
useful.) When the QMMM error message appeared on the bottom, SQM
terminated and ANTECHAMBER quited, even if like you word, bondtype
command did not complain... I also could know if the starting
structure was bad or good because I even could not enter SQM phase...
For the ligand, I directly ripped the structural information from
X-ray crystallograph of my receptor to do MD simulation for the
ligand-receptor pair. The pH environment of ligand and receptor is
around 7.0.
Could you know if something may go wrong according to the information
below? If you need more information for your referencing, do not
hesitate to let me know.
Sincerely,
Crystal
=========Information of sqm.out==================
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-09 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.1D-09
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is disabled.
| QMMM: Using internal diagonalization routine (diag_routine=1).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 C 17.4180 39.6130 64.1560
QMMM: 2 2 N 23.2430 40.7000 66.9120
QMMM: 3 3 C 23.1990 39.9700 68.0470
QMMM: 4 4 S 24.4660 38.8880 68.2630
QMMM: 5 5 C 25.1690 39.3930 66.7490
QMMM: 6 6 C 24.3770 40.3580 66.1730
QMMM: 7 7 C 24.6540 41.0370 64.8640
QMMM: 8 8 C 26.4420 38.8270 66.2310
QMMM: 9 9 C 27.6160 39.5410 66.7880
QMMM: 10 10 O 28.9050 39.0960 66.3640
QMMM: 11 11 N 19.5650 39.3350 65.1740
QMMM: 12 12 C 18.6210 40.2280 64.7150
QMMM: 13 13 N 18.7710 41.5250 64.7510
QMMM: 14 14 C 19.9280 42.0770 65.2910
QMMM: 15 15 N 20.0710 43.3990 65.3020
QMMM: 16 16 C 20.9490 41.1950 65.8320
QMMM: 17 17 C 20.7050 39.8420 65.7080
QMMM: 18 18 C 22.1730 41.7450 66.5390
QMMM: 19 19 P 30.2940 39.5950 66.9140
QMMM: 20 20 O 30.3800 41.0610 66.6910
QMMM: 21 21 O 31.2660 38.8010 66.1190
QMMM: 22 22 O 30.3310 39.2850 68.3790
QMMM: 23 23 H 16.7330 40.3920 63.8210
QMMM: 24 24 H 16.9320 39.0060 64.9200
QMMM: 25 25 H 17.6920 38.9820 63.3110
QMMM: 26 26 H 22.4020 40.0750 68.7680
QMMM: 27 27 H 25.5760 40.6420 64.4370
QMMM: 28 28 H 24.7600 42.1100 65.0270
QMMM: 29 29 H 23.8280 40.8530 64.1770
QMMM: 30 30 H 26.5020 37.7750 66.5090
QMMM: 31 31 H 26.4550 38.9110 65.1440
QMMM: 32 32 H 27.5230 40.5910 66.5120
QMMM: 33 33 H 27.5730 39.4700 67.8750
QMMM: 34 34 H 20.9050 43.8130 65.6920
QMMM: 35 35 H 19.3450 43.9890 64.9200
QMMM: 36 36 H 21.4600 39.1510 66.0540
QMMM: 37 37 H 22.6370 42.4830 65.8840
QMMM: 38 38 H 21.8490 42.2470 67.4500
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
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
On 11/11/11, case <case.biomaps.rutgers.edu> wrote:
> On Fri, Nov 11, 2011, Crystal.CHIA-YU Ku wrote:
>>
>> Running: /home/crystal/amber11/bin/bondtype -j full -i
>> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>> Info: Bond types are assigned for valence state 1 with penalty of 1
>> Running: /home/crystal/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
>> ANTECHAMBER_AC.AC -p gaff
>> Total number of electrons: 178; net charge: 1
>> Running: /home/crystal/amber11/bin/sqm -O -i sqm.in -o sqm.out
>> Error: cannot run "/home/crystal/amber11/bin/sqm -O -i sqm.in -o
>> sqm.out" of bcc() in charge.c properly, exit
>
> You need to look at the sqm.out file, which may (or may not) provide
> some evidence about what went wrong.
>
>>
>> I checked the structure of the ligand, and realized the two oxygen of
>> phosphate group had no hydrogen. Besides, one oxygen should be double
>> bond. I do not know if no hydrogen on oxygen of phosphate caused the
>> problem of running antechamber, so I trid Chimera to add H. But
>> Chimera does not add H to these two oxygen. Do you know how I can add
>> H to these two oxygen atom?
>
> Well, if Chimera doesn't want to add an H atom, maybe it is not needed(?)
> The fact that the bondtype command (above) did not complain is also a good,
> but by no means definitive, sign.
>
> Antechamber requires as input a good three-dimensional structure, with all
> hydrogens present and the correct total charge. Without knowing anything
> about your ligand, it's hard to say how to get from where you are to what
> you
> need.
>
>>
>> I also followed the method provide by the link. Since my ff99SB uses
>> ions94.lib, so I change ions94.cmd. But after changing ions94.cmd and
>> typing "tleap -f ions94.cmd", xleap still fails to generate prmtop and
>> inpcrd.
>
> Does the error in LEaP point to the Mg2+ ion? You certainly can't get a
> good
> prmtop until you solve the ligand problem discussed above. Try hard to
> parse
> the error messages and warnings that LEaP gives you. I know they may be
> hard
> to understand sometimes, but usually a careful reading pays dividends.
>
> ....dac
>
>
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Received on Mon Nov 14 2011 - 12:00:03 PST
