Here's what you need to do:
1. Collect all the atoms in each monosaccharide into separate
residues. Right now, there are just lists of atoms that might be
anywhere in the cyclodextrin molecule. It appears that the carbons
and oxygens might be arranged by monosaccharide, but the hydrogens are
all at the bottom. You don't need to re-number the atom serials, but
you do need to reorder them so that all the atoms for monosaccharide 1
are grouped together, and then for monosaccharide 2, etc. If the
positions of the hydrogens are not critical, it is acceptable to
delete them: leap will add them back in, but not necessarily in the
same positions. See also 1a...
1a. Ensure that the residues are split along the glycosidic linkage
between C1 and O4. That is, each C1 should be in a different residue
from the O4 to which it is bound.
2. Unless you are very lucky, you will also need to put TER cards
between each residue, so just do that.
3. Change the name of each residue to 4GA.
4. Give each residue a different number.
5. Rename the atoms in each residue so that the atom names match
perfectly the names in the 4GA residue. I have copied its residue
template at the bottom of this message for your convenience.
--- The section on oligosaccharides in the manual will help with steps
6-8. If you still cannot make it work, post the modified pdb file and
your leap commands.
6. In your leap input file, source leaprc.GLYCAM_06j-1 and load your pdb file.
7. Set explicit bond commands to re-connect each residue.
8. Have leap saveamberparm.
Here is the entry in the prep database (the residue template) for 4GA:
4GA INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 0.000 0.00 0.0000
2 DUMM DU M 1 0 -1 0.500 0.000 0.00 0.0000
3 DUMM DU M 2 1 0 1.296 74.264 0.00 0.0000
4 C1 Cg M 3 2 1 22.450 99.052 -130.25 0.5090
5 H1 H2 E 4 3 2 1.090 23.547 97.55 0.0000
6 C2 Cg M 4 3 2 1.556 111.527 7.33 0.2460
7 H2 H1 E 6 4 3 1.091 107.607 76.46 0.0000
8 O2 Oh S 6 4 3 1.465 111.499 -41.43 -0.7130
9 H2O Ho E 8 6 4 0.967 109.170 -40.31 0.4370
10 C3 Cg M 6 4 3 1.543 111.424 -164.87 0.2860
11 H3 H1 E 10 6 4 1.092 109.239 69.49 0.0000
12 O3 Oh S 10 6 4 1.452 108.531 -172.18 -0.6990
13 H3O Ho E 12 10 6 0.967 107.382 -43.08 0.4270
14 C4 Cg M 10 6 4 1.547 112.114 -52.22 0.2540
15 H4 H1 E 14 10 6 1.092 109.454 -66.45 0.0000
16 C5 Cg 3 14 10 6 1.543 111.254 54.50 0.2830
17 H5 H1 E 16 14 10 1.092 108.261 65.38 0.0000
18 C6 Cg 3 16 14 10 1.546 112.538 -174.79 0.2760
19 H62 H1 E 18 16 14 1.090 110.682 -45.93 0.0000
20 H61 H1 E 18 16 14 1.091 110.014 73.31 0.0000
21 O6 Oh S 18 16 14 1.444 110.823 -165.78 -0.6820
22 H6O Ho E 21 18 16 0.960 109.735 78.35 0.4180
23 O5 Os E 16 14 10 1.500 109.539 -52.54 -0.5740
24 O4 Os M 14 10 6 1.451 108.956 174.69 -0.4680
LOOP
O5 C1
DONE
On Fri, Apr 8, 2016 at 11:32 PM, CRISTIAN ROSSI PERARO
<cristianrossi.quimica.ufla.br> wrote:
> I am new to the area, hehe I am attaching the .pdb file here, I read in glycam.org site it is necessary to rename the residues to 4GB, but I do it when I carry the .pbd in Xleap him from various errors and molecule it is distorted.
> whem I use the gaff of some.
>
> I appreciate the attention.
>
> ----- Original Message -----
> From: Lachele Foley <lf.list.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Sat, 09 Apr 2016 00:07:24 -0300 (BRT)
> Subject: Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04
>
> I strongly recommend using GLYCAM06. Why use '04?
>
> This can certainly happen. Do you already have 3D coordinates? If
> you do, things will be much simpler for you. Note that there are
> examples of B-cyclodextrin coordinates in the PDB.
>
>
> On Fri, Apr 8, 2016 at 10:35 PM, CRISTIAN ROSSI PERARO
> <cristianrossi.quimica.ufla.br> wrote:
>> I'm not managing to prepare the .pdb B-cyclodextrin to use with glycam04.I need to change the .prepin file or do something ?can anybody help me ?thanks very much.
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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>
>
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Apr 08 2016 - 21:30:03 PDT
