Dear Ross,
Thanks a lot for that reply. I looked through the manual and it was
pretty useful. As I had told you earlier, my system has a non-standard
molecule:PIP2 (a lipid). So, I was trying to use antechamber to create the
topology file. I have the PDB file and a '.res' file for this molecule (a
sample of whihc is given below, pls have a look at it to see if its
readable in antechamber).
So when I say (to create a modified pdb file):
antechamber -i pip.pdb -fi pdb -o pip.mpdb -fo mpdb -c bcc -s 2
it says:
Running: /disk11/amber7/exe/mopac.sh ANTECHAMBER_MUL.MOP
ANTECHAMBER_MUL.OUT
/disk11/amber7/exe/mopac.sh[11]: /usr/local/bin/mopac: not found
Unable to find mopac charges in ANTECHAMBER_MUL.OUT
Next, I thought that this is because of a novel residue so i try
generating the modified PDB file for a regular protein, so when I say:
antechamber -i mod1a1h.pdb -fi pdb -o pro.mpdb -fo mpdb -c bcc -s 2
it says:
Running: /disk11/amber7/exe/mopac.sh ANTECHAMBER_MUL.MOP
ANTECHAMBER_MUL.OUT
/disk11/amber7/exe/mopac.sh[11]: /usr/local/bin/mopac: not found
Unable to find mopac charges in ANTECHAMBER_MUL.OUT
So my questions:
1) what is going wrong here?
2) secondly in both the cases, i use a standard BCC charge method. I dont
want to use that for my lipid PIP2. So, how can I ask it use the charges I
have in the .res file given below ( the set of rows starting with
-0.5689)? I tried using the '-rf all.res' addition to my command but it
says the same error as the two cases above.
I am trying to create a modified PDB file just to check if everything's
ok. My main goal is to create a prmtop file for the system.
I really appreciate your help anf efforts.
Thanks,
Nitin
####### all.res file for the lipid #########
INO INT 43 44 80 106 68 228
M OS O01 M CT C02 E HC H03 E HC H04 M CT C05 E HC H06 3
CT
C07 E HC H08 E HC H09 S OS O10 3 P P11 E O2 O12 E O2
O13 S
OS O14 B CT C15 E HC H16 3 CT C17 E HC H18 S OH O19 E HO
H20
3 CT C21 E HC H22 S OH O23 E HO H24 3 CT C25 E HC H26 S
OS
O27 3 P P28 E O2 O29 E O2 O30 E O2 O31 3 CT C32 E HC
H33 S
OS O34 3 P P35 E O2 O36 E O2 O37 E O2 O38 B CT C39 E HC
H40
S OH O41 E HO H42 M OS O43
1 2 2 3 2 4 2 5 5 6 5 7 5 43 7 8 7 9
7 10
10 11 11 12 11 13 11 14 14 15 15 16 15 17 15 39 17 18
17 19
17 21 19 20 21 22 21 23 21 25 23 24 25 26 25 27 25 32
27 28
28 29 28 30 28 31 32 33 32 34 32 39 34 35 35 36 35 37
35 38
39 40 39 41 41 42 -50 -50
1 2 3 1 2 4 1 2 5 2 5 6 2 5 7 2 5 43
3 2
4 3 2 5 4 2 5 5 7 8 5 7 9 5 7 10 6 5
7 6
5 43 7 10 11 7 5 43 8 7 9 8 7 10 9 7 10 10
11 12
10 11 13 10 11 14 11 14 15 12 11 13 12 11 14 13 11 14
14 15
16 14 15 17 14 15 39 15 17 18 15 17 19 15 17 21 15 39
32 15
39 40 15 39 41 16 15 17 16 15 39 17 19 20 17 21 22 17
21 23
17 21 25 17 15 39 18 17 19 18 17 21 19 17 21 21 23 24
21 25
26 21 25 27 21 25 32 22 21 23 22 21 25 23 21 25 25 27
28 25
32 33 25 32 34 25 32 39 26 25 27 26 25 32 27 28 29 27
28 30
27 28 31 27 25 32 29 28 30 29 28 31 30 28 31 32 34 35
32 39
40 32 39 41 33 32 34 33 32 39 34 35 36 34 35 37 34 35
38 34
32 39 36 35 37 36 35 38 37 35 38 39 41 42 40 39 41 -50
-50 -50
1 2 5 6 1 2 5 7 1 2 5 43 2 5 7 8 2 5
7 9
2 5 7 10 3 2 5 6 3 2 5 7 3 2 5 43 4 2
5 6
4 2 5 7 4 2 5 43 5 7 10 11 6 5 7 8 6 5
7 9
6 5 7 10 7 10 11 12 7 10 11 13 7 10 11 14 8 7
10 11
8 7 5 43 9 7 10 11 9 7 5 43 10 11 14 15 10 7
5 43
11 14 15 16 11 14 15 17 11 14 15 39 12 11 14 15 13 11
14 15
14 15 17 18 14 15 17 19 14 15 17 21 14 15 39 32 14 15
39 40
14 15 39 41 15 17 19 20 15 17 21 22 15 17 21 23 15 39
32 25
15 17 -21 25 15 39 32 33 15 39 32 34 15 39 41 42 16 15
17 18
16 15 17 19 16 15 17 21 16 15 39 32 16 15 39 40 16 15
39 41
17 21 23 24 17 21 25 26 17 21 25 27 17 15 39 32 17 21
-25 32
17 15 39 40 17 15 39 41 18 17 19 20 18 17 21 22 18 17
21 23
18 17 21 25 18 17 15 39 19 17 21 22 19 17 21 23 19 17
21 25
19 17 15 39 20 19 17 21 21 25 27 28 21 25 32 33 21 25
32 34
21 17 15 39 21 25 -32 39 22 21 23 24 22 21 25 26 22 21
25 27
22 21 25 32 23 21 25 26 23 21 25 27 23 21 25 32 24 23
21 25
25 27 28 29 25 27 28 30 25 27 28 31 25 32 34 35 25 32
39 40
25 32 39 41 26 25 27 28 26 25 32 33 26 25 32 34 26 25
32 39
27 25 32 33 27 25 32 34 27 25 32 39 28 27 25 32 32 34
35 36
32 34 35 37 32 34 35 38 32 39 41 42 33 32 34 35 33 32
39 40
33 32 39 41 34 32 39 40 34 32 39 41 35 34 32 39 40 39
41 42
-50 -50 -50 -50
43 43 3 4 43 6 42 8 9 42 42 12 13 42 42 16 42 18
20 20
42 22 24 24 42 26 31 31 29 30 31 42 33 38 38 36 37 38
42 40
42 42 43
0 1 2 2 2 5 5 7 7 7 10 11 11 11 14 15 15 17
17 19
17 21 21 23 21 25 25 27 28 28 28 25 32 32 34 35 35 35
32 39
39 41 5
0 1 1 2 1 3 0 2 1 4 0 2 1 5 1 6 0 5
1 7
1 8 0 7 1 9 0 7 1 10 1 11 1 12 0 11 1 13
0 11
1 14 1 15 1 16 0 15 1 17 1 18 0 17 1 19 1 20
0 17
1 21 1 22 0 21 1 23 1 24 0 21 1 25 1 26 0 25
1 27
1 28 1 29 0 28 1 30 0 28 1 31 0 25 1 32 1 33
0 32
1 34 1 35 1 36 0 35 1 37 0 35 1 38 0 32 1 39
1 40
0 39 1 41 1 42 0 15 1 39 0 5 1 43 2 0
7 9 5 4 7 5 8 4 3 6 7 3 2 10 16 8 14 7
6 1
11 6 5 1 13 6 8 4 2 1 1 10 5 7 4 2 1 1
3 2
1 1 1
2 3 4 5 6 7 43 3 4 5 6 7 8 9 10 43 4 5
6 7
43 5 6 7 43 6 7 8 9 10 11 43 7 8 9 10 43 8
9 10
11 12 13 14 43 9 10 11 43 10 11 43 11 12 13 14 15 43
12 13
14 15 16 17 39 13 14 15 14 15 15 16 17 18 19 21 32 39
40 41
16 17 18 19 20 21 22 23 25 32 33 34 39 40 41 42 17 18
19 21
32 39 40 41 18 19 20 21 22 23 24 25 26 27 32 39 40 41
19 20
21 22 23 25 39 20 21 22 23 25 39 21 22 23 24 25 26 27
28 32
33 34 39 23 24 25 26 27 32 24 25 26 27 32 25 26 27 28
29 30
31 32 33 34 35 39 40 41 27 28 32 33 34 39 28 29 30 31
32 33
34 39 29 30 31 32 30 31 31 0 33 34 35 36 37 38 39 40
41 42
34 35 39 40 41 35 36 37 38 39 40 41 36 37 38 39 37 38
38 0
40 41 42 41 42 42 0 0
-0.5689 0.6393 -0.0964 -0.0964 -0.4513 0.1893 0.1345 0.0448 0.0448 -0.5520
1.5088 -0.9414 -0.9414 -0.4555 -0.0601 0.1481 0.0193 0.1199 -0.7594 0.5251
0.0234 0.0693 -0.4413 0.3214 0.1581 0.1687 -0.4692 1.3342 -1.0003 -1.0003
-1.0003 0.1043 0.0901 -0.4601 1.2655 -0.9693 -0.9693 -0.9693 -0.0302 0.1845 -0.4776 0.3579 0.2588
1.50000 120.00000 0.00000 1.50000 109.00000 180.00000 1.00000 109.00000
180.00000 1.00000 109.00000 -60.00000 1.53000 111.10000 60.00000
1.00000
109.00000 51.10000 1.50000 109.00000 170.20000 1.00000 109.00000
60.00000
1.00000 109.00000 -60.00000 1.50000 120.00000 180.00000 1.60000
119.04000
65.40000 1.48000 108.20000-175.00000 1.48000 108.20000 -75.00000
1.50000
102.60000 75.60000 1.50000 109.00000 72.50000 1.00000 109.50000
49.30000
1.50000 109.00000 -72.50000 1.00000 109.50000 60.00000 1.41000
109.50000
-60.00000 0.96000 108.50000 60.00000 1.50000 109.00000 180.00000
1.00000
109.50000 -60.00000 1.41000 109.50000 180.00000 0.96000 108.50000
60.00000
1.50000 109.00000 60.00000 1.00000 109.50000 60.00000 1.42500
109.50000
-174.50000 1.50000 120.50000 -57.80000 1.48000 108.20000 60.00000
1.48000
108.20000 -43.50000 1.61000 108.20000-163.39999 1.50000 109.00000
-60.00000
1.00000 109.50000 -60.00000 1.42500 109.50000 177.30000 1.50000
120.50000
178.80000 1.48000 108.20000-162.20000 1.48000 108.20000 -42.40000
1.61000
108.20000 78.30000 1.50000 109.00000 60.00000 1.00000 109.50000
60.00000
1.41000 109.50000 180.00000 0.96000 108.50000 61.70000 1.22900
120.50000
-70.50000
On Mon, 22 Nov 2004, Ross Walker wrote:
> Dear Nitin,
>
> > 1) How can I create the parm file containing the topology and
> > parameter information for PIP2?
>
> See the amber tutorials - I have written one which explains how to use xleap
> to create a prmtop and inpcrd file for a system containing non-standard
> residues - you can modify this.
>
> http://amber.scripps.edu/tutorial/
>
> > 2) I have the pdb file only for the lipid "POPC" and I have the other
> > informattion (parameters and topology) in 'charmm' format.
> > Can I change
> > the charmm file into an appropriate (properly scaled) 'amber'
> > file format?
>
> Not easily (although somebody correct me if I am wrong here) as far as I
> know there is no automated way to do this. However, the charmm and amber
> force fields are sufficiently similar that you should be able to get a
> listing of the parameters for your system (atom types, bonds angle dihedrals
> etc) from the charmm topology file. You can then create yourself an amber
> frcmod file from this that you can load into xleap when creating the amber
> topology file.
>
> You should ideally calculate the charges using Amber's RESP method rather
> than using the charges from the charmm topology file - see the amber website
> for info on this.
>
> > Is there an amber topology and parameter file for this lipid
> > 'POPC' or any other lipid?
>
> There may be - try google and see if you get anything...
>
> > I am a complete novice in this regard so I would be very
> > thankful if the reply could be a detailed one.
>
> Go through the Amber Workshop tutorials and things will become a lot
> clearer.
>
> I hope this helps.
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
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Received on Tue Nov 23 2004 - 00:53:00 PST
