AMBER Archive (2009)

Subject: Re: [AMBER] Beginner question

From: Heath Watts (hwatts_at_geosc.psu.edu)
Date: Fri Feb 13 2009 - 19:20:46 CST

Thanks for your help and thanks for the link to glycam.com Florent.
Heath

On Fri, Feb 13, 2009 at 4:25 PM, Barbault Florent <
florent.barbault_at_univ-paris-diderot.fr> wrote:

> Hello,
>
> If you want created carbohydrates, you should have a look of glycam force
> field which is adapted to this sort of molecules. You could find an example
> of generation of a carbohydrate in the manual of amber 9. I also suggest to
> have a look on the website of glycam (www.glycam.com) in which there is a
> builder for carbohydrates.
>
> Hope this will help you
> Regards
> Florent Barbault
>
> On Fri, 13 Feb 2009 16:18:42 -0500
> Heath Watts <hwatts_at_geosc.psu.edu> wrote:
>
>> Hi,
>> I've worked through Ross Walker's tutorials and they were great. Now, I'm
>> trying to build a simple model of my own to run through the process. I
>> build
>> a model of D-glucose in Cerius 2 and saved it as a PDB file. I then
>> started
>> AMBER and used the loadpdb command. When the structure loads into AMBER,
>> I'm
>> getting the following message:
>>
>>
>> glucose=loadpdb "glucose.pdb"
>>>
>> Loading PDB file: ./glucose.pdb
>> Unknown residue: UNK number: 0 type: Terminal/last
>> ..relaxing end constraints to try for a dbase match
>> -no luck
>> Creating new UNIT for residue: UNK sequence: 0
>> Created a new atom named: C2 within residue: .R<UNK 0>
>> Created a new atom named: C3 within residue: .R<UNK 0>
>> Created a new atom named: C4 within residue: .R<UNK 0>
>> Created a new atom named: C5 within residue: .R<UNK 0>
>> Created a new atom named: C6 within residue: .R<UNK 0>
>> Created a new atom named: O7 within residue: .R<UNK 0>
>> Created a new atom named: O12 within residue: .R<UNK 0>
>> Created a new atom named: H13 within residue: .R<UNK 0>
>> Created a new atom named: H15 within residue: .R<UNK 0>
>> Created a new atom named: O16 within residue: .R<UNK 0>
>> Created a new atom named: O17 within residue: .R<UNK 0>
>> Created a new atom named: H18 within residue: .R<UNK 0>
>> Created a new atom named: H19 within residue: .R<UNK 0>
>> Created a new atom named: O20 within residue: .R<UNK 0>
>> Created a new atom named: C21 within residue: .R<UNK 0>
>> Created a new atom named: H22 within residue: .R<UNK 0>
>> Created a new atom named: O23 within residue: .R<UNK 0>
>> Created a new atom named: H26 within residue: .R<UNK 0>
>> Created a new atom named: H27 within residue: .R<UNK 0>
>> Created a new atom named: H28 within residue: .R<UNK 0>
>> Created a new atom named: H29 within residue: .R<UNK 0>
>> Created a new atom named: H30 within residue: .R<UNK 0>
>> Created a new atom named: H31 within residue: .R<UNK 0>
>> Created a new atom named: H32 within residue: .R<UNK 0>
>> total atoms in file: 24
>> The file contained 24 atoms not in residue templates
>>
>> When I type:
>> edit glucose
>> The model loads, but the bonds are not there. Because of this, I am not
>> able
>> to make the impcrd file. How can I make the pbd file so AMBER recognizes
>> its
>> residue templates?
>>
>> Here is the PDB I built:
>> REMARK 4 Mode COMPLIES WITH FORMAT V. 2.0
>> HETATM 1 C2 UNK 0 -1.221 0.492 -0.696 1.00 0.00
>> C
>> HETATM 2 C3 UNK 0 -0.143 -0.104 -0.025 1.00 0.00
>> C
>> HETATM 3 C4 UNK 0 0.958 0.757 -0.069 1.00 0.00
>> C
>> HETATM 4 C5 UNK 0 1.255 1.005 -1.410 1.00 0.00
>> C
>> HETATM 5 C6 UNK 0 0.132 1.571 -2.028 1.00 0.00
>> C
>> HETATM 6 O7 UNK 0 -0.889 0.750 -1.939 1.00 0.00
>> O
>> HETATM 7 O12 UNK 0 -0.153 2.708 -1.464 1.00 0.00
>> O
>> HETATM 8 3H1 UNK 0 0.329 1.725 -2.947 1.00 0.00
>> H
>> HETATM 9 5H1 UNK 0 1.994 1.604 -1.472 1.00 0.00
>> H
>> HETATM 10 O16 UNK 0 1.552 -0.112 -2.005 1.00 0.00
>> O
>> HETATM 11 O17 UNK 0 0.675 1.877 0.530 1.00 0.00
>> O
>> HETATM 12 8H1 UNK 0 1.705 0.350 0.360 1.00 0.00
>> H
>> HETATM 13 9H1 UNK 0 -0.383 -0.277 0.881 1.00 0.00
>> H
>> HETATM 14 O20 UNK 0 0.160 -1.224 -0.611 1.00 0.00
>> O
>> HETATM 15 C21 UNK 0 -1.593 1.673 -0.042 1.00 0.00
>> C
>> HETATM 16 2H2 UNK 0 -1.961 -0.108 -0.690 1.00 0.00
>> H
>> HETATM 17 O23 UNK 0 -2.591 2.219 -0.672 1.00 0.00
>> O
>> HETATM 18 6H2 UNK 0 0.514 3.232 -1.531 1.00 0.00
>> H
>> HETATM 19 7H2 UNK 0 0.888 -0.643 -1.956 1.00 0.00
>> H
>> HETATM 20 8H2 UNK 0 1.344 2.400 0.485 1.00 0.00
>> H
>> HETATM 21 9H2 UNK 0 -0.512 -1.746 -0.590 1.00 0.00
>> H
>> HETATM 22 0H3 UNK 0 -1.849 1.475 0.854 1.00 0.00
>> H
>> HETATM 23 1H3 UNK 0 -0.856 2.275 -0.034 1.00 0.00
>> H
>> HETATM 24 2H3 UNK 0 -2.356 2.395 -1.472 1.00 0.00
>> H
>> TER 25 UNK 0
>> END
>>
>> I realize that it contains no connectivity, but I've used pdb files from
>> other sources too, and the results are the same,except the bonds are
>> visible, but I still can't make an impcrd file. Here is one of those
>> downloaded pdb files:
>>
>> COMPND
>> REMARK 1 PDB to MMOD atom-numbering translation table; the mmod numbers
>> REMARK 1 pertain to the .dat file from which this file was created,
>> REMARK 1 not to one created from this file:
>> REMARK 1 PDB: 1 2 3 4 5 6 7 8 9
>> REMARK 1 MMOD: 1 2 3 4 5 6 7 8 9 /
>> REMARK 1 PDB: 10 11 12 13 14 15 16 17 18
>> REMARK 1 MMOD: 10 11 23 12 13 14 15 16 17 /
>> REMARK 1 PDB: 19 20 21 22 23 24
>> REMARK 1 MMOD: 18 19 20 21 22 24 /
>> HETATM 1 C01 UNK A 1 -10.447 3.465 0.000 0.00 0.00 0
>> HETATM 2 C02 UNK A 1 -11.071 4.006 1.273 0.00 0.00 0
>> HETATM 3 C03 UNK A 1 -12.577 4.148 1.128 0.00 0.00 0
>> HETATM 4 C04 UNK A 1 -12.891 4.988 -0.105 0.00 0.00 0
>> HETATM 5 C05 UNK A 1 -12.200 4.411 -1.349 0.00 0.00 0
>> HETATM 6 O06 UNK A 1 -10.802 4.239 -1.130 0.00 0.00 0
>> HETATM 7 O07 UNK A 1 -10.803 3.104 2.323 0.00 0.00 0
>> HETATM 8 O08 UNK A 1 -13.072 4.770 2.296 0.00 0.00 0
>> HETATM 9 O09 UNK A 1 -14.294 4.984 -0.281 0.00 0.00 0
>> HETATM 10 C10 UNK A 1 -12.311 5.317 -2.577 0.00 0.00 0
>> HETATM 11 O11 UNK A 1 -13.660 5.466 -2.961 0.00 0.00 0
>> HETATM 12 O23 UNK A 1 -9.045 3.478 0.138 0.00 0.00 0
>> HETATM 13 H12 UNK A 1 -9.995 3.339 2.755 0.00 0.00 0
>> HETATM 14 H13 UNK A 1 -12.863 4.206 3.024 0.00 0.00 0
>> HETATM 15 H14 UNK A 1 -13.704 6.000 -3.739 0.00 0.00 0
>> HETATM 16 H15 UNK A 1 -10.793 2.419 -0.156 0.00 0.00 0
>> HETATM 17 H16 UNK A 1 -10.626 4.997 1.513 0.00 0.00 0
>> HETATM 18 H17 UNK A 1 -13.037 3.141 1.020 0.00 0.00 0
>> HETATM 19 H18 UNK A 1 -12.542 6.032 0.061 0.00 0.00 0
>> HETATM 20 H19 UNK A 1 -12.653 3.423 -1.588 0.00 0.00 0
>> HETATM 21 H20 UNK A 1 -14.475 5.505 -1.044 0.00 0.00 0
>> HETATM 22 H21 UNK A 1 -11.886 6.317 -2.335 0.00 0.00 0
>> HETATM 23 H22 UNK A 1 -11.738 4.866 -3.418 0.00 0.00 0
>> HETATM 24 H24 UNK A 1 -8.822 2.951 0.906 0.00 0.00 0
>> CONECT 1 2 6 12 16
>> CONECT 2 1 3 7 17
>> CONECT 3 2 4 8 18
>> CONECT 4 3 5 9 19
>> CONECT 5 4 6 10 20
>> CONECT 6 5 1
>> CONECT 7 2 13
>> CONECT 8 3 14
>> CONECT 9 4 21
>> CONECT 10 5 11 22 23
>> CONECT 11 10 15
>> CONECT 12 1 24
>> CONECT 13 7
>> CONECT 14 8
>> CONECT 15 11
>> CONECT 16 1
>> CONECT 17 2
>> CONECT 18 3
>> CONECT 19 4
>> CONECT 20 5
>> CONECT 21 9
>> CONECT 22 10
>> CONECT 23 10
>> CONECT 24 12
>> END
>>
>> Any help is greatly appreicated. I'd really like to learn how to move
>> models
>> that I've built into AMBER.
>> Thanks,
>> Heath
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> -------------------------------------------------
> Dr Florent Barbault
> Maitre de conferences / Assistant professor
>
> NEW ADDRESS !!!
>
> Universite Paris Diderot
> Laboratoire ITODYS
> 15 rue Jean de Baïf, bâtiment Lavoisier
> 75013 Paris FRANCE
> http://www.itodys.univ-paris7.fr/
> tel : (33) 01-57-27-88-50
> e-mail : florent.barbault_at_univ-paris-diderot.fr
> -------------------------------------------------
>
>
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