Kirill Bessonov wrote:
Dear Gmx users,
I had been using Gromacs for couple of years and always found these
forums quite helpful. Right now again I have another question to ask
that I was not able to figure out yet myself and reading previous posts.
I need to the ffG53a6 forcefield to be able to recognize the
non-standard amino acid like AZE (Azetidine-2-carboxylic acid) which
closely resembles Proline, but lacks CH2 group in the ring of the
side-group, making the R-group a 4 member ring instead of 5. Thus, this
amino acid has very close chemical structure to the Proline which is
properly defined in the *.rtp file as below
[ PRO ]
[ atoms ]
N N 0.00000 0
CA CH1 0.00000 1
CB CH2R 0.00000 1
CG CH2R 0.00000 2
CD CH2R 0.00000 2
C C 0.450 3
O O -0.450 3
[ bonds ]
N CA gb_21
N CD gb_21
CA CB gb_27
CA C gb_27
CB CG gb_27
CG CD gb_27
C O gb_5
C +N gb_10
[ angles ]
; ai aj ak gromos type
-C N CA ga_31
-C N CD ga_31
CA N CD ga_21
N CA CB ga_13
N CA C ga_13
CB CA C ga_13
CA CB CG ga_13
CB CG CD ga_13
N CD CG ga_13
CA C O ga_30
CA C +N ga_19
O C +N ga_33
[ impropers ]
; ai aj ak al gromos type
N -C CA CD gi_1
CA N C CB gi_2
C CA +N O gi_1
[ dihedrals ]
; ai aj ak al gromos type
-CA -C N CA gd_14
-C N CA C gd_39
CA N CD CG gd_39
N CA CB CG gd_34
N CA C +N gd_40
CA CB CG CD gd_34
CB CG CD N gd_34
The question is how can I derive from this Proline definition topology
the corresponding topology for AZE? The problem is that I do know how to
You can use PRO as a framework, but you'll likely have to define completely new
angle and dihedral terms for the four-membered ring. No such group exists in
normal biomolecules, so likely the force field cannot handle it without
modification.
interpret the each column such as the "gromos definition" column gd_14,
etc, as well as other columns..... Where can I get information or
tutorials about this important issue on how to create own topology
files? Maybe someone can explain those columns in easy terms? What are
The terms are defined in ffbonded.itp:
; Dihedral-angle type code
; Force constant
; Phase shift
; Multiplicity
; Example of usage in terms of non-bonded atom types
;
;
; ICP(H)[N] CP[N] PD[N] NP[N]
;
#define gd_1 180.000 2.67 1
; CHn-CHn-CHn-OA (sugar) 0.6
Therefore, gd_1 is the type code, 180.000 is the force constant, 2.67 is the
phase shift, and 1 is the multiplicity. The comment line below this definition
is its example usage in terms of standard atom types/functional groups.
corresponding atoms referred by atom names in the final structure as the
there is not ASCI diagram of those as I've seen in AMBER tutorials?
The atom names used are standard nomenclature for amino acids.
Also I am interested in knowing on how the topology files are created
from scratch?
Sorry, I don't understand what you mean here.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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