Have you set up your ligand file sepearte to your ligand+complex pdb file?
On Tue, 28 Aug 2018 at 14:00, Antonio Amber Carlesso <
antonio.amber.carlesso.gmail.com> wrote:
> Hi all,
>
> I am trying to correctly prepare a protein with a ligand.
>
> I think I follow the tips from a previous post about it (
> http://archive.ambermd.org/200910/0258.html) but something is not working
> properly.
>
> Any idea what could be missing?
>
> And is there any additional “difficulties” if I would like to add more than
> one ligand?
>
>
>
> *> > source leaprc.ff14SB (for the protein part) *
>
> *done*
> *> > source leaprc.gaff (for the ligand part) *
>
> *done*
> *> > loadMol2 ligand.mol2 (where ligand.mol2 is created by antechamber) *
>
> *done*
>
> *> > complex = loadPDB complex.pdb (where complex.pdb has consistent
> coordinates *
> *> > of both the protein and the ligand, with the *
> *> > ligand residue and atom names the same as in *
> *> > the mol2 files loaded above. You *
> *> > should have a TER card separating protein and *
> *> > ligand.) *
> *> > *
> *done*
>
>
>
> *The complex PDB File seems respecting the two basic rules:*
>
> *-TER card separating protein and ligand*
>
> * -Ligand residue and atom names the same in the mol2 files
> loaded above*
>
>
>
>
>
> *final part of the complex PDB file:*
>
> ATOM 6581 HH33 NME A 964A 41.816 55.879 35.696 1.00
> 0.00 H
>
> *TER * 6582 NME A 964A
>
> HETATM 6583 *C21* 31J 1 62.646 44.388 0.248 1.00
> 0.00 C
>
> HETATM 6584 *C23* 31J 1 63.488 44.572 2.530 1.00
> 0.00 C
>
> HETATM 6585 *C01* 31J 1 61.681 49.585 8.264 1.00
> 0.00 C
>
> HETATM 6586 *O02* 31J 1 62.786 49.188 7.462 1.00
> 0.00 O
>
> HETATM 6587 *C03* 31J 1 62.765 49.769 6.161 1.00
> 0.00 C
>
> HETATM 6588 *C04* 31J 1 64.147 49.628 5.499 1.00
> 0.00 C
>
> HETATM 6589 *O05* 31J 1 64.481 48.284 5.154 1.00
> 0.00 O
>
> HETATM 6590 *C06* 31J 1 63.814 47.776 3.999 1.00
> 0.00 C
>
> HETATM 6591 *C07* 31J 1 64.669 46.662 3.373 1.00 0.00
> C
>
> HETATM 6592 *C08* 31J 1 63.968 45.940 2.212 1.00
> 0.00 C
>
> HETATM 6593 *C09 *31J 1 63.791 46.459 0.969 1.00
> 0.00 C
>
> HETATM 6594 *C10 *31J 1 64.312 47.837 0.560 1.00
> 0.00 C
>
> HETATM 6595 *C11* 31J 1 63.074 45.684 -0.075 1.00
> 0.00 C
>
> HETATM 6596 *C12* 31J 1 62.785 46.195 -1.344 1.00
> 0.00 C
>
> HETATM 6597 *C13* 31J 1 62.096 45.438 -2.286 1.00
> 0.00 C
>
> HETATM 6598 *O14* 31J 1 61.853 46.030 -3.506 1.00
> 0.00 O
>
> HETATM 6599 *C15* 31J 1 60.481 46.239 -3.830 1.00
> 0.00 C
>
> HETATM 6600 *C16* 31J 1 61.721 44.118 -1.986 1.00
> 0.00 C
>
> HETATM 6601 *O17* 31J 1 61.114 43.377 -2.977 1.00
> 0.00 O
>
> HETATM 6602 *C18* 31J 1 61.988 43.580 -0.709 1.00
> 0.00 C
>
> HETATM 6603 *O22* 31J 1 62.862 43.879 1.524 1.00
> 0.00 O
>
> HETATM 6604 *O24* 31J 1 63.587 43.952 3.590 1.00
> 0.00 O
>
> HETATM 6605 *C* 31J 1 61.586 42.170 -0.402 1.00
> 0.00 C
>
> HETATM 6606 *O* 31J 1 61.781 41.588 0.663 1.00
> 0.00 O
>
> HETATM 6607 *H17* 31J 1 60.886 42.475 -2.749 1.00
> 0.00 H
>
> HETATM 6608 *H* 31J 1 61.078 41.642 -1.207 1.00
> 0.00 H
>
> HETATM 6609 *H011* 31J 1 61.791 49.188 9.272 1.00
> 0.00 H
>
> HETATM 6610 *H012* 31J 1 60.741 49.210 7.854 1.00
> 0.00 H
>
> HETATM 6611 *H013* 31J 1 61.615 50.670 8.356 1.00
> 0.00 H
>
> HETATM 6612 *H031* 31J 1 62.523 50.833 6.217 1.00
> 0.00 H
>
> HETATM 6613 *H032* 31J 1 61.988 49.301 5.555 1.00
> 0.00 H
>
> HETATM 6614 *H041* 31J 1 64.906 49.988 6.194 1.00
> 0.00 H
>
> HETATM 6615 *H042* 31J 1 64.221 50.280 4.627 1.00
> 0.00 H
>
> HETATM 6616 *H061* 31J 1 63.646 48.561 3.260 1.00
> 0.00 H
>
> HETATM 6617 *H062* 31J 1 62.829 47.393 4.263 1.00
> 0.00 H
>
> HETATM 6618 *H071* 31J 1 64.977 45.967 4.157 1.00
> 0.00 H
>
> HETATM 6619 *H072* 31J 1 65.608 47.086 3.015 1.00
> 0.00 H
>
> HETATM 6620 *H101* 31J 1 64.898 48.335 1.329 1.00
> 0.00 H
>
> HETATM 6621 *H102* 31J 1 63.480 48.497 0.313 1.00
> 0.00 H
>
> HETATM 6622 *H103* 31J 1 64.958 47.752 -0.315 1.00
> 0.00 H
>
> HETATM 6623 *H12* 31J 1 63.076 47.196 -1.625 1.00
> 0.00 H
>
> HETATM 6624 *H151* 31J 1 60.413 46.921 -4.677 1.00
> 0.00 H
>
> HETATM 6625 *H152* 31J 1 59.926 46.685 -3.003 1.00
> 0.00 H
>
> HETATM 6626 *H153* 31J 1 59.986 45.315 -4.126 1.00
> 0.00 H
>
> CONECT 1 2 4 5 6
>
> CONECT 2 1 3 3
>
> CONECT 3 2 2
>
> CONECT 4 1
>
> CONECT 5 1
>
> CONECT 6 1
>
> CONECT 6576 6577 6578
>
> CONECT 6577 6576 6579 6580 6581
>
> CONECT 6578 6576
>
> CONECT 6579 6577
>
> CONECT 6580 6577
>
> CONECT 6581 6577
>
> CONECT 6583 6595 6602 6602 6603
>
> CONECT 6584 6592 6603 6604 6604
>
> CONECT 6585 6586 6609 6610 6611
>
> CONECT 6586 6585 6587
>
> CONECT 6587 6586 6588 6612 6613
>
> CONECT 6588 6587 6589 6614 6615
>
> CONECT 6589 6588 6590
>
> CONECT 6590 6589 6591 6616 6617
>
> CONECT 6591 6590 6592 6618 6619
>
> CONECT 6592 6584 6591 6593 6593
>
> CONECT 6593 6592 6592 6594 6595
>
> CONECT 6594 6593 6620 6621 6622
>
> CONECT 6595 6583 6593 6596 6596
>
> CONECT 6596 6595 6595 6597 6623
>
> CONECT 6597 6596 6598 6600 6600
>
> CONECT 6598 6597 6599
>
> CONECT 6599 6598 6624 6625 6626
>
> CONECT 6600 6597 6597 6601 6602
>
> CONECT 6601 6600 6607
>
> CONECT 6602 6583 6583 6600 6605
>
> CONECT 6603 6583 6584
>
> CONECT 6604 6584 6584
>
> CONECT 6605 6602 6606 6606 6608
>
> CONECT 6606 6605 6605
>
> CONECT 6607 6601
>
> CONECT 6608 6605
>
> CONECT 6609 6585
>
> CONECT 6610 6585
>
> CONECT 6611 6585
>
> CONECT 6612 6587
>
> CONECT 6613 6587
>
> CONECT 6614 6588
>
> CONECT 6615 6588
>
> CONECT 6616 6590
>
> CONECT 6617 6590
>
> CONECT 6618 6591
>
> CONECT 6619 6591
>
> CONECT 6620 6594
>
> CONECT 6621 6594
>
> CONECT 6622 6594
>
> CONECT 6623 6596
>
> CONECT 6624 6599
>
> CONECT 6625 6599
>
> CONECT 6626 6599
>
> END
>
>
>
>
>
> *And the .mol2 file*
>
> .<TRIPOS>MOLECULE
>
> 31J
>
> 44 51 1 0 0
>
> SMALL
>
> bcc
>
>
>
>
>
> .<TRIPOS>ATOM
>
> 1 C21 62.6460 44.3880 0.2480 c3 1 31J
> 0.249800
>
> 2 C23 63.4880 44.5720 2.5300 c3 1 31J
> 0.559400
>
> 3 C01 61.6810 49.5850 8.2640 c3 1 31J
> 0.117700
>
> 4 O02 62.7860 49.1880 7.4620 os 1 31J
> -0.424600
>
> 5 C03 62.7650 49.7690 6.1610 c3 1 31J
> 0.095400
>
> 6 C04 64.1470 49.6280 5.4990 c3 1 31J
> 0.127400
>
> 7 O05 64.4810 48.2840 5.1540 os 1 31J
> -0.422600
>
> 8 C06 63.8140 47.7760 3.9990 c3 1 31J
> 0.129400
>
> 9 C07 64.6690 46.6620 3.3730 c3 1 31J
> -0.042400
>
> 10 C08 63.9680 45.9400 2.2120 c3 1 31J
> -0.187000
>
> 11 C09 63.7910 46.4590 0.9690 c3 1 31J
> 0.055000
>
> 12 C10 64.3120 47.8370 0.5600 c3 1 31J
> -0.086100
>
> 13 C11 63.0740 45.6840 -0.0750 c3 1 31J
> -0.179000
>
> 14 C12 62.7850 46.1950 -1.3440 c3 1 31J
> 0.006300
>
> 15 C13 62.0960 45.4380 -2.2860 c3 1 31J
> 0.050800
>
> 16 O14 61.8530 46.0300 -3.5060 os 1 31J
> -0.350600
>
> 17 C15 60.4810 46.2390 -3.8300 c3 1 31J
> 0.111700
>
> 18 C16 61.7210 44.1180 -1.9860 c3 1 31J
> 0.259800
>
> 19 O17 61.1140 43.3770 -2.9770 oh 1 31J
> -0.511800
>
> 20 C18 61.9880 43.5800 -0.7090 c3 1 31J
> -0.288000
>
> 21 O22 62.8620 43.8790 1.5240 os 1 31J
> -0.344600
>
> 22 O24 63.5870 43.9520 3.5900 os 1 31J
> -0.428600
>
> 23 C 61.5860 42.1700 -0.4020 c3 1 31J
> 0.428900
>
> 24 O 61.7810 41.5880 0.6630 os 1 31J
> -0.472600
>
> 25 H17 60.8860 42.4750 -2.7490 ho 1 31J
> 0.470000
>
> 26 H 61.0780 41.6420 -1.2070 h2 1 31J
> 0.097700
>
> 27 H011 61.7910 49.1880 9.2720 h1 1 31J
> 0.034700
>
> 28 H012 60.7410 49.2100 7.8540 h1 1 31J
> 0.034700
>
> 29 H013 61.6150 50.6700 8.3560 h1 1 31J
> 0.034700
>
> 30 H031 62.5230 50.8330 6.2170 h1 1 31J
> 0.036700
>
> 31 H032 61.9880 49.3010 5.5550 h1 1 31J
> 0.036700
>
> 32 H041 64.9060 49.9880 6.1940 h1 1 31J
> 0.060700
>
> 33 H042 64.2210 50.2800 4.6270 h1 1 31J
> 0.060700
>
> 34 H061 63.6460 48.5610 3.2600 h1 1 31J
> 0.033700
>
> 35 H062 62.8290 47.3930 4.2630 h1 1 31J
> 0.033700
>
> 36 H071 64.9770 45.9670 4.1570 hc 1 31J
> 0.077700
>
> 37 H072 65.6080 47.0860 3.0150 hc 1 31J
> 0.077700
>
> 38 H101 64.8980 48.3350 1.3290 hc 1 31J
> 0.064033
>
> 39 H102 63.4800 48.4970 0.3130 hc 1 31J
> 0.064033
>
> 40 H103 64.9580 47.7520 -0.3150 hc 1 31J
> 0.064033
>
> 41 H12 63.0760 47.1960 -1.6250 hc 1 31J
> 0.121700
>
> 42 H151 60.4130 46.9210 -4.6770 h1 1 31J
> 0.047367
>
> 43 H152 59.9260 46.6850 -3.0030 h1 1 31J
> 0.047367
>
> 44 H153 59.9860 45.3150 -4.1260 h1 1 31J
> 0.047367
>
> .<TRIPOS>BOND
>
> 1 1 13 1
>
> 2 1 20 1
>
> 3 1 20 1
>
> 4 1 21 1
>
> 5 2 10 1
>
> 6 2 21 1
>
> 7 2 22 1
>
> 8 2 22 1
>
> 9 3 4 1
>
> 10 3 27 1
>
> 11 3 28 1
>
> 12 3 29 1
>
> 13 4 5 1
>
> 14 5 6 1
>
> 15 5 30 1
>
> 16 5 31 1
>
> 17 6 7 1
>
> 18 6 32 1
>
> 19 6 33 1
>
> 20 7 8 1
>
> 21 8 9 1
>
> 22 8 34 1
>
> 23 8 35 1
>
> 24 9 10 1
>
> 25 9 36 1
>
> 26 9 37 1
>
> 27 10 11 1
>
> 28 10 11 1
>
> 29 11 12 1
>
> 30 11 13 1
>
> 31 12 38 1
>
> 32 12 39 1
>
> 33 12 40 1
>
> 34 13 14 1
>
> 35 13 14 1
>
> 36 14 15 1
>
> 37 14 41 1
>
> 38 15 16 1
>
> 39 15 18 1
>
> 40 15 18 1
>
> 41 16 17 1
>
> 42 17 42 1
>
> 43 17 43 1
>
> 44 17 44 1
>
> 45 18 19 1
>
> 46 18 20 1
>
> 47 19 25 1
>
> 48 20 23 1
>
> 49 23 24 1
>
> 50 23 24 1
>
> 51 23 26 1
>
> .<TRIPOS>SUBSTRUCTURE
>
> 1 31J 1 TEMP 0 **** **** 0 ROOT
>
>
>
>
>
>
>
>
>
>
>
> *And here if it could be useful to someone the overall series of commands!*
>
> Welcome to LEaP!
>
> (no leaprc in search path)
>
> > source leaprc.ff14SB
>
> ----- Source: /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.ff14SB
>
> ----- Source of /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.ff14SB
> done
>
> Log file: ./leap.log
>
> Loading parameters: /Users/Antonio/Desktop/amber18/dat/leap/parm/parm10.dat
>
> Reading title:
>
> PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
>
> Loading parameters:
> /Users/Antonio/Desktop/amber18/dat/leap/parm/frcmod.ff14SB
>
> Reading force field modification type file (frcmod)
>
> Reading title:
>
> ff14SB protein backbone and sidechain parameters
>
> Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/amino12.lib
>
> Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/aminoct12.lib
>
> Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/aminont12.lib
>
> Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/nucleic12.lib
>
> Loading library:
> /Users/Antonio/Desktop/amber18/dat/leap/lib/atomic_ions.lib
>
> Loading library: /Users/Antonio/Desktop/amber18/dat/leap/lib/solvents.lib
>
> > source leaprc.gaff
>
> ----- Source: /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.gaff
>
> ----- Source of /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.gaff
> done
>
> Log file: ./leap.log
>
> Loading parameters: /Users/Antonio/Desktop/amber18/dat/leap/parm/gaff.dat
>
> Reading title:
>
> AMBER General Force Field for organic molecules (Version 1.81, May 2017)
>
> > loadMol2 MKC.mol2
>
> Loading Mol2 file: ./MKC.mol2
>
> Reading MOLECULE named 31J
>
> > complex=loadPDB complex.pdb
>
> Loading PDB file: ./complex.pdb
>
>
>
> Warning: Unknown residue: 31J number: 407 type: Terminal/last
>
> ..relaxing end constraints to try for a dbase match
>
>
>
> Warning: -no luck
>
> Creating new UNIT for residue: 31J sequence: 966
>
> Created a new atom named: C21 within residue: .R<31J 966>
>
> Created a new atom named: C23 within residue: .R<31J 966>
>
> Created a new atom named: C01 within residue: .R<31J 966>
>
> Created a new atom named: O02 within residue: .R<31J 966>
>
> Created a new atom named: C03 within residue: .R<31J 966>
>
> Created a new atom named: C04 within residue: .R<31J 966>
>
> Created a new atom named: O05 within residue: .R<31J 966>
>
> Created a new atom named: C06 within residue: .R<31J 966>
>
> Created a new atom named: C07 within residue: .R<31J 966>
>
> Created a new atom named: C08 within residue: .R<31J 966>
>
> Created a new atom named: C09 within residue: .R<31J 966>
>
> Created a new atom named: C10 within residue: .R<31J 966>
>
> Created a new atom named: C11 within residue: .R<31J 966>
>
> Created a new atom named: C12 within residue: .R<31J 966>
>
> Created a new atom named: C13 within residue: .R<31J 966>
>
> Created a new atom named: O14 within residue: .R<31J 966>
>
> Created a new atom named: C15 within residue: .R<31J 966>
>
> Created a new atom named: C16 within residue: .R<31J 966>
>
> Created a new atom named: O17 within residue: .R<31J 966>
>
> Created a new atom named: C18 within residue: .R<31J 966>
>
> Created a new atom named: O22 within residue: .R<31J 966>
>
> Created a new atom named: O24 within residue: .R<31J 966>
>
> Created a new atom named: C within residue: .R<31J 966>
>
> Created a new atom named: O within residue: .R<31J 966>
>
> Created a new atom named: H17 within residue: .R<31J 966>
>
> Created a new atom named: H within residue: .R<31J 966>
>
> Created a new atom named: H011 within residue: .R<31J 966>
>
> Created a new atom named: H012 within residue: .R<31J 966>
>
> Created a new atom named: H013 within residue: .R<31J 966>
>
> Created a new atom named: H031 within residue: .R<31J 966>
>
> Created a new atom named: H032 within residue: .R<31J 966>
>
> Created a new atom named: H041 within residue: .R<31J 966>
>
> Created a new atom named: H042 within residue: .R<31J 966>
>
> Created a new atom named: H061 within residue: .R<31J 966>
>
> Created a new atom named: H062 within residue: .R<31J 966>
>
> Created a new atom named: H071 within residue: .R<31J 966>
>
> Created a new atom named: H072 within residue: .R<31J 966>
>
> Created a new atom named: H101 within residue: .R<31J 966>
>
> Created a new atom named: H102 within residue: .R<31J 966>
>
> Created a new atom named: H103 within residue: .R<31J 966>
>
> Created a new atom named: H12 within residue: .R<31J 966>
>
> Created a new atom named: H151 within residue: .R<31J 966>
>
> Created a new atom named: H152 within residue: .R<31J 966>
>
> Created a new atom named: H153 within residue: .R<31J 966>
>
> total atoms in file: 6625
>
> The file contained 44 atoms not in residue templates
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Received on Tue Aug 28 2018 - 07:00:03 PDT
