AMBER Archive (2009)

Subject: Re: [AMBER] Beginner question

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Feb 13 2009 - 15:24:37 CST

I suggest building models with standard Amber residues first- like an
amino acid.
get those working so you are comfortable making your own files. then,
if you want to do glucose you will need to (1) tell leap what force
field to use and (2) probably change your pdb file so the residue info
is not "UNK" but instead matches the name of glucose in the force
field you are using. you might run into more problems then, but at
least you will get you farther and perhaps see more error messages.

On Fri, Feb 13, 2009 at 4:18 PM, 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
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