[gmx-users] sridhar: How to include topologies for unusual/phosphorylated residues occurring within the protein chain.
Paul Barrett
barrett at biop.ox.ac.uk
Fri May 16 11:05:01 CEST 2003
Using Grahams force field sounds like a good idea. However if you want
to do it yourself here is how I did it for phosphorylated Threonine.
1) open the appropriate .rtp file e.g. ffG43a1.rtp
2) make a copy of the existing entry for the residue you want to
phosphorylate it.
here are the notes I made as I did it...comments welcome if anyone
doesnt like how I did it!
; TPO which follows is phosphorylated Threonine and was derived thus:
; 1) take THR entry
; 2) add P, O1P, O2P, O3P atoms
; 3) remove HG1 atom
; 4) assign partial charges to give an overall molecule -2 charge
; with this charge localised on the Phosphate group.
; 5) add bonds for OG1 to P and the OxPs. took bond tpyes from [ DADE ]
; 6) likewise took angle types from [ DADE ]
; 7) removed final dihedral which contained H1 (had considered changing
it for
; P but dont want to limit Phoshphate group too much)
3) you will need to add the new residue to the file aminoacids.dat if
you want the residue to be recognised as part of the protein in
subsequent analysis. Make sure you increment the count on the top line
of aminoacids.dat. dont put any comments in aminoacids.dat becuase it
has unpredictable effects on results.
4) update the hydrogen database entry too if you are expecting pdb2gmx
or protonate to work properly.
I *think* that was it...!
Below is the full text for the phosphorylated Threonine from my
ffG43a1.rtp
Paul Barrett
University of Oxford
Dept of Biochemistry
barrett at biop.ox.ac.uk
[ TPO ]
[ atoms ]
N N -0.28000 0
H H 0.28000 0
CA CH1 0.00000 1
CB CH1 0.15000 2
OG1 OA -0.54800 2
P P 0.79800 2
O1P OM -0.80000 2
O2P OM -0.80000 2
O3P OM -0.80000 2
CG2 CH3 0.00000 3
C C 0.380 4
O O -0.380 4
[ bonds ]
N H gb_2
N CA gb_20
CA C gb_26
C O gb_4
C +N gb_9
CA CB gb_26
CB OG1 gb_17
CB CG2 gb_26
P O1P gb_23
P O2P gb_23
P O3P gb_23
P OG1 gb_27
[ angles ]
; ai aj ak gromos type
-C N H ga_31
H N CA ga_17
-C N CA ga_30
N CA C ga_12
CA C +N ga_18
CA C O ga_29
O C +N ga_32
N CA CB ga_12
C CA CB ga_12
CA CB OG1 ga_12
CA CB CG2 ga_14
OG1 CB CG2 ga_14
OG1 P O1P ga_23
OG1 P O2P ga_23
OG1 P O3P ga_23
CB OG1 P ga_27
O1P P O2P ga_28
O1P P O3P ga_28
O2P P O3P ga_28
[ impropers ]
; ai aj ak al gromos type
N -C CA H gi_1
C CA +N O gi_1
CA N C CB gi_2
CB OG1 CG2 CA gi_2
[ dihedrals ]
; ai aj ak al gromos type
-CA -C N CA gd_4
-C N CA C gd_19
N CA C +N gd_20
N CA CB OG1 gd_17
>Dear Gromacs users,
>
>I am a graduate student at Centre for DNA Fingerprinting and Diagnostics,
>Hyderabad, India. I am currently working on Dynamic simulation studies
>using GROMACS software.
>
>In my current work I want to do simulation of a protein containing
>PhosphoSerine. Regarding this I went through the Article "Gromacs Tutorial
>for Drug-Enzyme Complex" which has shown clearly step-by-step how to
>include new topologies for drug/ligand molecules.
>
>By I was not successful in running the dynamics. I got topology for
>Phosphoserine from PRODRG server. The "Drug-Enzyme complex" tutorial was
>specific for ligands/Drugs that do not form part of the protein chain. But
>if I want to include topology for special residues like Phosphoserine
>which occur within the protein chain, how to do it?
>
>I tried according to the tutorial but was unsuccessful all the time.
>I'll be very grateful if you can outline me the procedure to be
>followed in such cases.
>
>Thankyou very much.
>
>sridhar.
>
>
>
>On Sat, 10 May 2003, Mr.Sridhar wrote:
>
>>
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>
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