[gmx-users] Adding TPO and SEP to G53a6 Forcefield
lalithkumar
lalithkumar07 at gmail.com
Sat Feb 22 12:33:32 CET 2014
Dear gromacs users,
I have got two phosphorylated residues Tyrosine (TPO) and Serine (SEP) in A
and B chains of my heterotrimer homology model. So, I went with the step by
step process suggested by GROMACS at the
link:http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
Please dont mind, to be clear, I would like to place each and every single
step that I have made and pasted in ff folder.
1. I copied a folder named gromos53a6.ff and file residuetypes.dat from the
gromacs installed directory and pasted in the present working directory to
trial the modifications.
2. I have added topologies for TPO and SEP to the .rtp file at the end of
file as below: (I am very happy if anyone corrects me if there were any
mistakes)
[ TPO ]
[ atoms ]
N N -0.31000 0
H H 0.31000 0
CA CH1 0.00000 1
CB CH1 0.00000 2
OG1 OA -0.50000 2
P P 0.90000 2
O1P OP -0.80000 2
O2P OP -0.80000 2
O3P OP -0.80000 2
CG2 CH3 0.00000 3
C C 0.450 4
O O -0.450 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
OG1 P gb_27
P O1P gb_23
P O2P gb_23
P O3P gb_23
[ 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
CB OG1 P ga_25
OG1 P O1P ga_13
OG1 P O2P ga_13
OG1 P O3P ga_13
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
CA CB OG1 P gd_14
CB OG1 P O1P gd_11
[ SEP ]
[ atoms ]
N N -0.31000 0
H H 0.31000 0
CA CH1 0.00000 1
CB CH2 0.00000 2
OG OA -0.50000 2
P P 0.90000 2
O1P OP -0.80000 2
O2P OP -0.80000 2
O3P OP -0.80000 2
C C 0.450 3
O O -0.450 3
[ 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 OG gb_17
OG P gb_27
P O1P gb_23
P O2P gb_23
P O3P gb_23
[ 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 OG ga_12
CB OG P ga_25
OG P O1P ga_13
OG P O2P ga_13
OG P O3P ga_13
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
[ 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 OG gd_17
CA CB OG P gd_14
CB OG P O1P gd_11
3. Created an appropriate entries in .hdb files at the end of file for
hydrogen addition
TPO 1
1 1 H N -C CA
SEP 1
1 1 H N -C CA
4. Addition of atom types in .atp file at the end
OP 15.99940 ; phosphate oxygen (P=O) selon hansson aqvist jmb 97
and in ffnonbonded.itp file added:
OP 8 0.000 0.000 A 0.0022153 3.8239e-06
5. I dont think these are new bonded types and so not disturbed ffbonded.itp
file.
6. Added TPO and SEP to residuetypes.dat file alphabetically and specifying
it as protein
7. No special connectivity and so not edited specbond.dat
After doing these steps, I called the forcefield within working directory
while pdb2gmx prompted. No errors and my file got processed until genbox.
The command issued was:
g_pdb2gmx -ignh -f protein.pdb -o protein_pdb2gmx.pdb -p
protein_topology.top -water spce
g_editconf -bt cubic -f protein_pdb2gmx.pdb -o protein_editconf.pdb -d 1.0
-c
g_genbox -cp protein_editconf.pdb -cs spc216.gro -o protein_genbox.pdb -p
protein_topology.top
g_grompp -f EM.mdp -c protein_genbox.pdb -p protein_topology.top -o
protein_ions.tpr
and here, I get the following errors:
Ignoring obsolete mdp entry 'cpp'
Generated 222 of the 1653 non-bonded parameter combinations
ERROR 1 [file AMPK_topology_Protein_chain_A.itp, line 15435]:
No default LJ-14 types
ERROR 2 [file AMPK_topology_Protein_chain_A.itp, line 15436]:
No default LJ-14 types
ERROR 3 [file AMPK_topology_Protein_chain_A.itp, line 15437]:
No default LJ-14 types
ERROR 4 [file AMPK_topology_Protein_chain_B.itp, line 7610]:
No default LJ-14 types
ERROR 5 [file AMPK_topology_Protein_chain_B.itp, line 7611]:
No default LJ-14 types
ERROR 6 [file AMPK_topology_Protein_chain_B.itp, line 7612]:
No default LJ-14 types
I am not quite where my bond types went wrong, these lines in my .itp files
are corresponding to atoms listed below:
15435 1923 1926
15436 1923 1927
15437 1923 1928
ATOM 1920 N TPO A 183 68.232 63.098 68.923 1.00 0.00
ATOM 1921 H TPO A 183 68.988 63.061 69.576 1.00 0.00
ATOM 1922 CA TPO A 183 67.034 62.439 69.431 1.00 0.00
ATOM 1923 CB TPO A 183 67.071 62.360 70.916 1.00 0.00
ATOM 1924 OG1 TPO A 183 68.205 61.626 71.328 1.00 0.00
ATOM 1925 P TPO A 183 69.170 62.266 72.397 1.00 0.00
ATOM 1926 O1P TPO A 183 70.456 61.480 72.420 1.00 0.00
ATOM 1927 O2P TPO A 183 68.524 62.221 73.762 1.00 0.00
ATOM 1928 O3P TPO A 183 69.457 63.705 72.029 1.00 0.00
ATOM 1929 CG2 TPO A 183 65.822 61.647 71.391 1.00 0.00
ATOM 1930 C TPO A 183 65.781 63.123 68.984 1.00 0.00
ATOM 1931 O TPO A 183 65.536 64.269 69.348 1.00 0.00
which states CB connected phosphate group oxygens, if i am correct... but
how it happened is i dont know
similar is the case with next 3 errors that I have not added here.
I request if anyone could highlight the errors with my procedure and provide
a needful information to rectify it. Also, I am excited to know, Is there
any chance, to get g53a6ff prepared files for phosphorylated residues.
please, let me know for any further information
Many thanks in advance
sincerely,
Lalith Kumar K
Research Associate,
University of Hyderabad Campus
India
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