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 - 06:30:03 PDT
