I have of course used antechamber and parmchk to get prepin and frcmod(showed below), otherwise I wouldn't post this. Sorry, I haven't mentioned it (as obvious).
I've used initial compound with all atoms including hydrogens for it.
The problem maybe is in how ligand PDB is prepared.
Best regards,
Andrew
remark goes here
MASS
BOND
ANGLE
DIHE
c3-cc-ca-ca 1 2.550 180.000 2.000 same as X -c2-ca-X
ca-ca-cc-cd 1 2.550 180.000 2.000 same as X -c2-ca-X
IMPROPER
ca-n -c -o 10.5 180.0 2.0 General improper torsional angle (2 general atom types)
c -ca-ca-ca 1.1 180.0 2.0 Using default value
ca-ca-ca-ha 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
c -c -n -c3 1.1 180.0 2.0 Using default value
c3-n -c -o 10.5 180.0 2.0 General improper torsional angle (2 general atom types)
c3-ca-cc-cd 1.1 180.0 2.0 Using default value
ca-ca-ca-cc 1.1 180.0 2.0 Using default value
ca-ca-ca-na 1.1 180.0 2.0 Using default value
ca-cd-na-hn 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
c3-cc-cd-na 1.1 180.0 2.0 Using default value
NONBON
-------------------------
0 0 2
This is a remark line
molecule.res
RES INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 O2 o M 3 2 1 1.540 111.208 180.000 -0.612700
5 C8 c M 4 3 2 1.216 34.519 -26.639 0.738000
6 C4 ca M 5 4 3 1.461 123.849 45.899 -0.144800
7 C3 ca M 6 5 4 1.381 130.401 0.723 -0.060900
8 H24 ha E 7 6 5 1.084 121.018 -0.299 0.156000
9 C2 ca M 7 6 5 1.399 117.190 179.327 -0.116500
10 H25 ha E 9 7 6 1.089 119.785 -179.455 0.146300
11 C1 ca M 9 7 6 1.411 120.841 0.488 -0.113700
12 H26 ha E 11 9 7 1.089 119.454 -179.987 0.146600
13 C6 ca M 11 9 7 1.398 120.817 0.063 -0.060200
14 H1 ha E 13 11 9 1.085 121.594 179.748 0.161600
15 C5 ca M 13 11 9 1.381 117.214 -0.410 -0.139500
16 C7 c M 15 13 11 1.461 130.503 179.484 0.722500
17 O1 o E 16 15 13 1.215 123.953 -2.860 -0.560500
18 N1 n M 16 15 13 1.369 106.621 178.630 -0.520100
19 C9 c3 M 18 16 15 1.453 124.226 178.198 0.104000
20 H22 h1 E 19 18 16 1.095 108.145 -129.174 0.069200
21 H23 h1 E 19 18 16 1.093 108.523 -11.069 0.060000
22 C10 c3 M 19 18 16 1.523 111.864 109.991 -0.101800
23 H20 hc E 22 19 18 1.094 110.361 -37.192 0.063600
24 H21 hc E 22 19 18 1.085 107.625 -150.601 0.057200
25 C11 c3 M 22 19 18 1.535 112.179 87.750 -0.084500
26 H18 hc E 25 22 19 1.096 108.821 48.430 0.047200
27 H19 hc E 25 22 19 1.091 110.252 -67.106 0.039300
28 C12 c3 M 25 22 19 1.534 112.670 170.743 -0.076400
29 H16 hc E 28 25 22 1.094 109.447 -59.614 0.067900
30 H17 hc E 28 25 22 1.095 110.019 56.787 0.047100
31 C13 c3 M 28 25 22 1.530 112.291 -179.557 -0.148400
32 H14 hc E 31 28 25 1.092 110.088 -160.394 0.075500
33 H15 hc E 31 28 25 1.097 108.566 -43.244 0.052200
34 C14 c M 31 28 25 1.519 114.436 75.144 0.652900
35 O3 o E 34 31 28 1.226 123.423 -31.309 -0.620300
36 N2 n M 34 31 28 1.383 112.983 151.392 -0.559700
37 H13 hn E 36 34 31 1.011 117.221 10.859 0.313200
38 C15 c3 M 36 34 31 1.457 121.995 167.106 0.091900
39 H11 h1 E 38 36 34 1.096 106.560 48.990 0.040100
40 H12 h1 E 38 36 34 1.096 106.888 -65.911 0.080200
41 C16 c3 M 38 36 34 1.532 115.850 170.261 -0.037400
42 H9 hc E 41 38 36 1.098 108.064 59.654 0.053100
43 H10 hc E 41 38 36 1.093 110.510 174.792 0.057000
44 C17 cc M 41 38 36 1.504 114.673 -60.677 -0.158800
45 C18 ca M 44 41 38 1.436 126.393 -66.531 -0.085500
46 C19 ca M 45 44 41 1.410 134.165 -1.765 -0.057200
47 H8 ha E 46 45 44 1.085 120.286 -1.203 0.147000
48 C20 ca M 46 45 44 1.400 119.116 177.823 -0.055500
49 Br1 br E 48 46 45 1.892 119.430 -178.739 -0.101500
50 C21 ca M 48 46 45 1.392 121.294 0.504 -0.093700
51 H7 ha E 50 48 46 1.088 120.390 -179.786 0.142200
52 C22 ca M 50 48 46 1.397 120.566 -0.431 -0.144700
53 H6 ha E 52 50 48 1.085 120.788 -178.598 0.135200
54 C23 ca M 52 50 48 1.400 117.561 0.110 -0.038100
55 N3 na M 54 52 50 1.374 129.761 -178.593 -0.202400
56 H5 hn E 55 54 52 1.010 124.047 0.634 0.317400
57 C24 cd M 55 54 52 1.371 110.567 178.075 -0.007400
58 C25 c3 M 57 55 54 1.483 121.271 -177.048 -0.057900
59 H2 hc E 58 57 55 1.092 111.493 32.529 0.059600
60 H3 hc E 58 57 55 1.091 111.344 152.555 0.060600
61 H4 hc E 58 57 55 1.092 109.773 -87.956 0.055800
LOOP
N1 C8
C5 C4
C24 C17
C23 C18
IMPROPER
C4 N1 C8 O2
C8 C5 C4 C3
C4 C2 C3 H24
C1 C3 C2 H25
C6 C2 C1 H26
C1 C5 C6 H1
C7 C6 C5 C4
C5 N1 C7 O1
C7 C9 N1 C8
C13 N2 C14 O3
C14 C15 N2 H13
C16 C18 C17 C24
C19 C23 C18 C17
C18 C20 C19 H8
Br1 C19 C20 C21
C20 C22 C21 H7
C21 C23 C22 H6
C18 C22 C23 N3
C23 C24 N3 H5
C25 C17 C24 N3
DONE
STOP
11.03.10, 10:50, "Billy Miller III" <brmilleriii.gmail.com>:
> The ligand contains parameters that are not defined in the AMBER force field
> you are utilizing. You should use antechamber and parmchk to define these
> parameters in prepin and frcmod files. There is a good tutorial explaining
> the steps involved here (
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_five/create_prmtop.htm
> ).
>
> Good luck!
>
> -Bill Miller
>
> On Thu, Mar 11, 2010 at 10:39 AM, Andrew Voronkov wrote:
>
> > Dear Amber users,
> > I have problem while saving parametrization for protein-ligand complex. I
> > remember that I ve solved once somehow this problem and it is related either
> > to ligand formatting or hydrogens etc. But I can't remember how I ve solved
> > it. Here is the ligand file and error log. I can also send PDB of protein
> > but it seems to be ok with other ligands.
> >
> > Best regards,
> > Andrew
> >
> >
> > Checking Unit.
> > Building topology.
> > Building atom parameters.
> > Building bond parameters.
> > Could not find bond parameter for: cf - br
> > Building angle parameters.
> > Could not find angle parameter: br - cf - cf
> > Could not find angle parameter: ce - cf - br
> > Could not find angle parameter: ce - c3 - c2
> > Could not find angle parameter: ce - c3 - h1
> > Could not find angle parameter: ce - c3 - n3
> > Building proper torsion parameters.
> > ** No torsion terms for ce-ce-c3-c2
> > ** No torsion terms for ce-ce-c3-h1
> > ** No torsion terms for ce-ce-c3-n3
> > ** No torsion terms for c2-ce-c3-c2
> > ** No torsion terms for c2-ce-c3-h1
> > ** No torsion terms for c2-ce-c3-n3
> > Building improper torsion parameters.
> > total 814 improper torsions applied
> > Building H-Bond parameters.
> > Parameter file was not saved.
> > Quit
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
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>
>
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Received on Fri Mar 12 2010 - 04:30:03 PST
