Dear Urszula,
> I prepared the library for my non standard sugar-lys molecule, the
> FF atom types were also set. However after running leap I am getting
> still errors about missing parameters ...
>
> I attached the .off and pdb file...
> Could someone help me with that?
First, you do not need to transform a mol2 file into an off file as
both files have the same role in the LEaP program: a force field
library file format...
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
&
http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
&
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
I first corrected the atom names to avoid duplicated atom names in
your residue... (this should have been done by Ante_R.E.D.)
I also corrected the atom names to give names that 'make sense'; i.e.
name for instance the C2 atom (IUPAC nomenclature) of your
monosaccharide C2 (& not C4 as it was); etc... Try always to use atom
names easy/quickly understandable (convenient when you will use the
ptraj program to analyze your trajectories).
Then, I looked at the FF atom types in the OFF file; I found several errors:
atom names atom types
H5 H2 (& not H1)
O1 OS (& not O)
CE CT (Amber types)
HE1/HE2 HP
etc...
I also calculated the total charge of your unit using LEaP:
> charge MGR
Total unperturbed charge: 0.999800
I guess you used R.E.D. Server/R.E.D. IV; so rounding off error
corrections are not yet implemented; should be available soon... I
corrected your mol2 file so that you get an integer charge value. See
below ***!
16 HE1 -0.649429 4.488144 0.023487 HP 1 MGR 0.1115 ***!
17 HE2 -1.405649 3.352473 1.132925 HP 1 MGR 0.1115 ***!
See the corrected mol2 file below...
Once you have correctly defined the atom names (usually done when you
create your PDB input file _before_ using Ante_R.E.D.) and the atom
types (using a LEaP script so that you can easily choose which FF you
want to use) you can indeed load the FF parameters of your choice...
I corrected your mol2 file so that you have GLYCAM FF atom types for
the mono-saccharidic part and AMBER FF atom types for the amino-acid
part; you might decide to adopt a different strategy...
I hope this helps...
regards, Francois
Urszula: you need to understand what is an atom name and what is an
atom type... Knowing by heart the atom types of the FF you wish to use
is always convenient - and do not rely only on the program(s) you use...
.<TRIPOS>MOLECULE
MGR
44 44 1 0 1
SMALL
USER_CHARGES
.<TRIPOS>ATOM
1 N 3.580012 1.189673 0.326553 N 1 MGR -0.3642 ****
2 H 4.010848 1.843263 -0.291437 H 1 MGR 0.2812 ****
3 CA 2.601506 0.282586 -0.254995 CT 1 MGR -0.0659 ****
4 HA 2.180349 -0.270708 0.570735 H1 1 MGR 0.0783 ****
5 C 3.301670 -0.692027 -1.209829 C 1 MGR 0.6478 ****
6 O 3.348204 -0.476121 -2.391407 O 1 MGR -0.5785 ****
7 CB 1.490633 1.037201 -0.977728 CT 1 MGR -0.0216 ****
8 HB1 0.835117 0.307991 -1.434098 HC 1 MGR 0.0546 ****
9 HB2 1.912684 1.621291 -1.788142 HC 1 MGR 0.0546 ****
10 CG 0.684902 1.937284 -0.035603 CT 1 MGR -0.0393 ****
11 HG1 1.276834 2.801916 0.250029 HC 1 MGR 0.0432 ****
12 HG2 0.453019 1.413343 0.885912 HC 1 MGR 0.0432 ****
13 CD -0.603820 2.432652 -0.688075 CT 1 MGR -0.0457 ****
14 HD -0.366237 2.800211 -1.680250 H1 1 MGR 0.1447 ****
15 CE -1.242509 3.587870 0.090840 CT 1 MGR -0.0199 ****
16 HE1 -0.649429 4.488144 0.023487 HP 1 MGR 0.1115 ***!
17 HE2 -1.405649 3.352473 1.132925 HP 1 MGR 0.1115 ***!
18 NZ -2.597051 3.878326 -0.494971 N3 1 MGR -0.2009 ****
19 HZ1 -2.549603 3.998167 -1.496779 H 1 MGR 0.2673 ****
20 HZ2 -3.004760 4.715780 -0.106280 H 1 MGR 0.2673 ****
21 HZ3 -3.230376 3.093955 -0.309777 H 1 MGR 0.2673 ****
22 O1 -1.590440 1.456327 -0.925375 OS 1 MGR -0.2387 ****
23 C1 -1.962655 0.531306 0.041455 CG 1 MGR 0.0235 ****
24 H1 -1.728980 0.895387 1.041953 H2 1 MGR 0.1201 ****
25 O5 -1.283287 -0.648710 -0.192055 OS 1 MGR -0.3084 ****
26 C5 -1.675763 -1.730813 0.646224 CG 1 MGR -0.0265 ****
27 H5 -1.586143 -1.428741 1.688839 H1 1 MGR 0.1043 ****
28 C6 -0.709649 -2.881289 0.390729 CG 1 MGR 0.1881 ****
29 H61 0.308329 -2.526552 0.513548 H1 1 MGR 0.0513 ****
30 H62 -0.818460 -3.235812 -0.623498 H1 1 MGR 0.0513 ****
31 O6 -1.004624 -3.941227 1.250907 OH 1 MGR -0.5904 ****
32 HO6 -0.453518 -3.913769 2.019675 HO 1 MGR 0.3961 ****
33 C4 -3.130861 -2.070031 0.328883 CG 1 MGR 0.1544 ****
34 H4 -3.457062 -2.906540 0.928441 H1 1 MGR 0.1079 ****
35 O4 -3.279700 -2.439138 -1.007183 OH 1 MGR -0.5621 ****
36 HO4 -2.679563 -1.951325 -1.556022 HO 1 MGR 0.4037 ****
37 C3 -3.996683 -0.852074 0.670513 CG 1 MGR 0.0541 ****
38 H3 -3.893694 -0.666156 1.744612 H1 1 MGR 0.0970 ****
39 O3 -5.316802 -1.135651 0.349741 OH 1 MGR -0.5188 ****
40 HO3 -5.890567 -0.415651 0.573103 HO 1 MGR 0.3690 ****
41 C2 -3.475247 0.364183 -0.087257 CG 1 MGR 0.1360 ****
42 H2 -3.725612 0.257253 -1.131716 H1 1 MGR 0.1145 ****
43 O2 -4.087281 1.579731 0.344494 OH 1 MGR -0.5649 ****
44 HO2 -4.310954 1.530267 1.266411 HO 1 MGR 0.4020 ****
.<TRIPOS>BOND
1 1 2 1
2 1 3 1
3 3 4 1
4 3 5 1
5 3 7 1
6 5 6 1
7 7 8 1
8 7 9 1
9 7 10 1
10 10 11 1
11 10 12 1
12 10 13 1
13 13 14 1
14 13 15 1
15 13 22 1
16 15 16 1
17 15 17 1
18 15 18 1
19 18 19 1
20 18 20 1
21 18 21 1
22 22 23 1
23 23 24 1
24 23 25 1
25 23 41 1
26 25 26 1
27 26 27 1
28 26 28 1
29 26 33 1
30 28 29 1
31 28 30 1
32 28 31 1
33 31 32 1
34 33 34 1
35 33 35 1
36 33 37 1
37 35 36 1
38 37 38 1
39 37 39 1
40 37 41 1
41 39 40 1
42 41 42 1
43 41 43 1
44 43 44 1
.<TRIPOS>SUBSTRUCTURE
1 MGR 1 **** 0 **** ****
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Received on Thu Apr 26 2012 - 09:00:03 PDT
