Here's what I used for MgATP - I got the prep & frcmod files from a download site
http://www.pharmacy.manchester.ac.uk/bryce/amber. I've attached it as
lig.pdb. Note how MG is listed. That's crucial, as I said before. How are you generating the input for antechamber, by the way? I've done a ligand tautomer with a charge before - I created a .mol2 file for it from Schrodinger Maestro [we use Glide] & that worked OK.
The file leapit.rc contains the commands for sleap - just type sleap & then source leapit.rc & it all happens. Here's what the commands do:
The next 2 lines load the GAFF & ff99SB forcefields
source leaprc.gaff
source leaprc.ff99SB
This line loads the prepi file I downloaded for ATP [replace with your antechamber-generated stuff]
loadAmberPrep atp.prepi
This line loads the frcmod file I downloaded:
lig = loadAmberParams atp.frcmod
Here I'm loading the protein+ligand, then the protein only, then the ligand only. Because I want to do MMGBSA when I'm all done. However, Amber Tools 15 has a utility that splits a prmtop/inpcrd pair into ligand & receptor, so this isn't needed any more - only the first load is needed.
pl = loadpdb mapr.pdb
p = loadpdb ns.pdb
l = loadpdb lig.pdb
Here I'm saving the unsolvated, separate parts for future MMGBSA work. Again, no longer needed because of ante-MMGBSA.py
saveAmberParm l mgatp.prmtop mgatp.inpcrd
saveAmberParm p ns.prmtop ns.inpcrd
saveAmberParm pl mgatpprnw.prmtop mgatpprnw.inpcrd
Solvate with an orthorhombic box 12A from protein surface
solvateBox pl TIP3PBOX 12.0
Neutralize
addions pl Na+ 0
Add ions for ionic strength of 0.15M -- # of ions calculated from # of waters added & # used to neutralize. Note that I've had some issues with sleap
correctly computing the charge on a system & have had to remove that command & add the right combination of ions manually.
addions pl Na+ 25 Cl- 25
Save the solvated system:
saveAmberParm pl mgatppr.prmtop mgatppr.inpcrd
Hope this helps!
Irene
> Date: Mon, 14 Nov 2011 14:42:43 -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 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
> >> >
> >>
> >> _______________________________________________
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> >
>
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Received on Tue Nov 15 2011 - 11:30:02 PST
