Hi Irene,
Thank you for your relpy. However, my ligand pdb file never contains
MG. I tried to assign net charge +1 by the flag -nc but this way has
not worked. SQM always crashs and antechamber quits.
MG ion is another problem when I load pdb file of my receptor-ligand
pair, xleap cannot recognize two MG ions and the ligand. I tried to
remove the connectivity of the two MG ions, which means I let two MG
ions stand alone. But this way has not worked. I also modifed the
ions94.cmd; however, this way has not made success. I always get error
message like this:
FATAL: Atom .R<MG 89>.A<MG 1> does not have a type.
FATAL: Atom .R<MG 90>.A<MG 1> does not have a type.
Could I ask you how do you incorporate the antechamber result of your
ligand to your receptor in xleap?
Sincerely,
Crystal
On 11/14/11, Irene Newhouse <einew.hotmail.com> wrote:
>
> Antechamber absolutely crashes every time you have an ion. You can, however,
> create your ligand without the MG usingantechamber and then manually put
> back the MG into the ligand pdb file you use with sleap or xleap. That is
> how I didMg-ATP as a ligand myself earlier this year. The reason you can
> consider this as a valid work-around is that the Mg interacts mostly via
> electrostatic charge. It's not a particularly good work-around, as you might
> expect the presence ofa +2 charge to redistribute the charges in its
> neighborhood, but it's what you have to do to get it to work at all. Look in
> the data files for AMBER for the correct way to name the MG - that's
> crucial, & until I did that check, it wasn't workingfor me at all.
> Unfortunately I've already turned the computer on which I did that work off
> for the day & don't really wantto bring it back up. Irene NewhousePost-docU
> of Hawaii
> > Date: Mon, 14 Nov 2011 11:52:12 -0800
>> From: crystal.chia.yu.gmail.com
>> To: amber.ambermd.org
>> Subject: Re: [AMBER] Problems of generating prmtop and inpcrd files for
>> ligand-receptor with two Mg2+ ions --please help
>>
>> 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
>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 14 2011 - 15:00:04 PST
