[gmx-users] Adding TPO and SEP to G53a6 Forcefield
Justin Lemkul
jalemkul at vt.edu
Sat Feb 22 15:49:57 CET 2014
On 2/22/14, 6:31 AM, lalithkumar wrote:
> 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
>
The error indicates you are missing 1-4 interactions, which are listed in
[pairtypes] in ffnonbonded.itp. Gromos96 uses a matrix of different possible
parameter combinations to determine how 1-4 pairs interact. Since in the force
field, gen-pairs is set to "no," you have to manually specify all the possible
1-4 interactions. Since you added a new atom type, you have to add new 1-4
interactions in [pairtypes].
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
More information about the gromacs.org_gmx-users
mailing list