Hi Parker,
Following to the amber's tutorial I've faced with some problem during
preparation of my protein-ligand complex.
Firstly I've dock my ligand within the protein and minimize complex using
Chimera (using amber 99sb params)
Then I've parametrize my ligand following tutorial obtaining cGMP for its
deprotonated (-1) form
antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2 -nc -1
> check GUA
Checking 'GUA'....
WARNING: The unperturbed charge of the unit: -0.997000 is not zero.
Checking parameters for unit 'GUA'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
Than I've loaded my protein
> protein = loadpdb protein_h.pdb
Loading PDB file: ./protein_h.pdb
total atoms in file: 1590
Leap added 1585 missing atoms according to residue templates:
1585 H / lone pairs
> check protein
Checking 'protein'....
WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
Warning: Close contact of 1.477463 angstroms between .R<TYR 18>.A<HH 15>
and .R<ARG 52>.A<HE 15>
Checking parameters for unit 'protein'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 2
Unit is OK.
but I've obtained error when I've tried to load complex (just added
coordines ligand.pdb to the bottom of the protein.pdb)
> complex = loadpdb complex_h.pdb
Loading PDB file: ./complex_h.pdb
Created a new atom named: O2' within residue: .R<DG3 207>
total atoms in file: 1624
Leap added 1586 missing atoms according to residue templates:
1586 H / lone pairs
The file contained 1 atoms not in residue templates
> check complex
Checking 'complex'....
ERROR: The unperturbed charge of the unit: -2.692100 is not integral.
WARNING: The unperturbed charge of the unit: -2.692100 is not zero.
FATAL: Atom .R<DG3 207>.A<O2' 35> does not have a type.
Warning: Close contact of 1.477463 angstroms between .R<TYR 18>.A<HH 15>
and .R<ARG 52>.A<HE 15>
Warning: Close contact of 1.015789 angstroms between .R<DG3 207>.A<H2'1 31>
and .R<DG3 207>.A<O2' 35>
Warning: Close contact of 1.436767 angstroms between .R<DG3 207>.A<C2' 30>
and .R<DG3 207>.A<O2' 35>
Checking parameters for unit 'complex'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 2 Warnings: 4
Here you can see that new oxygen have been added to the last protein's TYR
aa
Created a new atom named: O2' within residue: .R<DG3 207>
Below you can also see end fragment of the PDB of my complex
ATOM 3154 N TYR 206 -10.805 -25.054 0.980 1.00
0.00 N
ATOM 3155 CA TYR 206 -10.572 -26.123 1.974 1.00
0.00 C
ATOM 3156 C TYR 206 -9.157 -26.733 2.020 1.00
0.00 C
ATOM 3157 O TYR 206 -8.785 -27.594 1.190 1.00
0.00 O
ATOM 3158 CB TYR 206 -11.695 -27.164 1.788 1.00
0.00 C
ATOM 3159 CG TYR 206 -12.023 -28.038 2.986 1.00
0.00 C
ATOM 3160 CD1 TYR 206 -12.525 -27.450 4.163 1.00
0.00 C
ATOM 3161 CD2 TYR 206 -11.942 -29.441 2.883 1.00
0.00 C
ATOM 3162 CE1 TYR 206 -12.947 -28.259 5.238 1.00
0.00 C
ATOM 3163 CE2 TYR 206 -12.368 -30.256 3.952 1.00
0.00 C
ATOM 3164 CZ TYR 206 -12.873 -29.665 5.128 1.00
0.00 C
ATOM 3165 OH TYR 206 -13.302 -30.450 6.152 1.00
0.00 O
ATOM 3166 OXT TYR 206 -8.401 -26.369 2.947 1.00
0.00 O1-
TER
HETATM 3177 P GUA 227 -1.531 -21.786 -3.023
1.00292.81 P
HETATM 3178 O1P GUA 227 -1.186 -22.731 -1.938
1.00292.81 O
HETATM 3179 O2P GUA 227 -0.560 -20.683 -3.051
1.00292.81 O
HETATM 3180 O5' GUA 227 -1.422 -22.635 -4.355
1.00292.81 O
HETATM 3181 C5' GUA 227 -2.464 -23.595 -4.639
1.00292.81 C
HETATM 3182 H5' GUA 227 -2.245 -24.031 -5.622
1.00292.81 H
HETATM 3183 H5'' GUA 227 -2.459 -24.364 -3.858
1.00292.81 H
HETATM 3184 C4' GUA 227 -3.805 -22.866 -4.641
1.00292.81 C
HETATM 3185 H4' GUA 227 -3.792 -22.075 -5.374
1.00292.81 H
HETATM 3186 O4' GUA 227 -4.965 -23.675 -4.824
1.00292.81 O
HETATM 3187 C1' GUA 227 -6.091 -22.839 -4.404
1.00292.81 C
HETATM 3188 H1' GUA 227 -6.511 -22.338 -5.285
1.00292.81 H
HETATM 3189 N9 GUA 227 -7.167 -23.649 -3.869
1.00292.81 N
HETATM 3190 C4 GUA 227 -7.155 -24.662 -2.958
1.00292.81 C
HETATM 3191 N2 GUA 227 -5.949 -27.214 -0.929
1.00292.81 N
HETATM 3192 H21 GUA 227 -6.411 -28.065 -0.657
1.00292.81 H
HETATM 3193 H22 GUA 227 -5.094 -27.291 -1.452
1.00292.81 H
HETATM 3194 N3 GUA 227 -6.207 -25.357 -2.218
1.00292.81 N
HETATM 3195 C2 GUA 227 -6.777 -26.301 -1.451
1.00292.81 C
HETATM 3196 N1 GUA 227 -8.108 -26.606 -1.311
1.00292.81 N
HETATM 3197 H1 GUA 227 -8.424 -27.237 -0.586
1.00292.81 H
HETATM 3198 C6 GUA 227 -9.081 -26.021 -2.013
1.00292.81 C
HETATM 3199 O6 GUA 227 -10.247 -26.335 -1.851
1.00292.81 O
HETATM 3200 C5 GUA 227 -8.543 -24.982 -2.890
1.00292.81 C
HETATM 3201 N7 GUA 227 -9.281 -24.188 -3.695
1.00292.81 N
HETATM 3202 C8 GUA 227 -8.444 -23.393 -4.312
1.00292.81 C
HETATM 3203 H8 GUA 227 -8.745 -22.649 -5.032
1.00292.81 H
HETATM 3204 C2' GUA 227 -5.520 -21.755 -3.453
1.00292.81 C
HETATM 3205 H2'' GUA 227 -6.077 -21.744 -2.510
1.00292.81 H
HETATM 3206 O2' GUA 227 -5.578 -20.505 -4.159
1.00292.81 O
HETATM 3207 H2' GUA 227 -5.391 -19.728 -3.532
1.00292.81 H
HETATM 3208 C3' GUA 227 -4.070 -22.248 -3.287
1.00292.81 C
HETATM 3209 H3' GUA 227 -4.042 -23.026 -2.505
1.00292.81 H
HETATM 3210 O3' GUA 227 -3.043 -21.255 -3.021
1.00292.81 O
END
What corrections should I do?
Thanks for help,
James
2014-04-28 16:19 GMT+04:00 de Waal, Parker <Parker.DeWaal.vai.org>:
> Hi James,
>
> I'd recommend following the antechamber tutorial on the amebrmd website:
> http://ambermd.org/tutorials/basic/tutorial4b/ . It is fairly
> comprehensive and easy to follow. Additionally if you wanted to generate
> RESP charges semi-empirically, as well as optimized geometry, for cGMP I
> would highly recommend using REDS http://q4md-forcefieldtools.org/REDS/ .
> Sign up for an account to use Guassian09.
>
> Best,
> Parker
> ________________________________________
> From: James Starlight [jmsstarlight.gmail.com]
> Sent: Monday, April 28, 2014 8:02 AM
> To: AMBER Mailing List
> Subject: [AMBER] Simulation of protein- cyclic nucleotide complex
>
> Dear Amber Users!
>
>
> I'd like to perform simulation of the water-soluble protein in complex with
> the small ligand where ligand is the cyclic nucleotide guanosine
> monophosphate (cGMP). The output trajectory of this simulation will be
> further processed by means of
> http://scanmail.trustwave.com/?c=129&d=1MPe07wUGAo8aOhatZ8CMsCq5aiGHUg1nTyBAF7YKQ&u=http%3a%2f%2fmmpbsa%2epyanalysis. Could you suggest me the
> reason amber's param sets for such ligand and protein as well as proper
> tutorial for protein-ligand simulation?
>
> Thanks for help,
>
> James
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Received on Tue Apr 29 2014 - 03:00:02 PDT
