GROMACS version:2020
GROMACS modification: Yes/No yes
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Dear Gromacs users
I have a small molecule (ligand) for which I took parameters from acpype and add in local force field directory in gromacs. I build rtp, hdb files for the residue because I want to get a merged topology of ligand and protein. I have done what is mentioned in gromacs manual for adding a new residue to forcefield but still I am getting this problem:-
‘Atom type C1 (residue G6P) not found in atomtype database’
Can you please help me to sort out this problem. Also understanding the format of hdb and rtp file is not a simple and easy I am not very much sure what I build is correct or otherwise. Can you please help me to solve this problem.
I have added following atomtypes in atomtypes.atp file:-
;[ atomtypes ]
;name mass charge ptype sigma epsilon Amb
c3 12.01000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094
oh 16.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104
os 16.00000 0.00000 A 3.00001e-01 7.11280e-01 ; 1.68 0.1700
p5 30.97000 0.00000 A 3.74177e-01 8.36800e-01 ; 2.10 0.2000
o 16.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100
h2 1.00800 0.00000 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157
h1 1.00800 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157
ho 1.00800 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000
hdbfile:-
G6P 10
1 2 HO1 O1 C1 C2
1 2 HO2 O2 C2 C1
1 3 HO3 O3 C3 C2
1 2 HO4 O4 C4 C5
1 5 H1 C1 O1 C2 O5
1 5 H2 C2 O2 C3 C1
1 5 H3 C3 O3 C4 C2
1 5 H4 C4 O4 C5 C3
1 5 H5 C5 O5 C6 C4
2 6 H6 C6 C5 O6
thank you @jalemkul for your suggestion.
What about the header line of rtp file. I just copied what was there in default rtp files but actually could not understand very much about my molecule how should I set the header of rtp in it which is mentioned as below:-
[ bondedtypes ]
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 1 9 4 1 3 1 0
Regards.
Sadaf
Dear @jalemkul
I followed the manual but still, I have confusion please correct me where I am wrong. e.g. I am getting the following error
Fatal error:
Atom H51 not found in rtp database in residue LIG, it looks a bit like H5
I don’t have any H51 residue in my pdb file for the LIG molecule I am not getting why I am getting this error
I have build hdb file as below:-
LIG 11
1 2 H7 O1 C1 C2
1 2 H8 O2 C2 C1
1 2 H9 O3 C3 C2
1 2 H10 O4 C4 C5
1 5 H C1 O1 C2 O5
1 5 H1 C2 O2 C3 C1
1 5 H2 C3 O3 C4 C2
1 5 H3 C4 O4 C5 C3
1 5 H4 C5 O5 C6 C4
2 6 H5 C6 c5 O6
2 6 H6 C6 C5 O6
H5 and H6 are attached to the same C atom which is C6. Could you please correct me where I am wrong. I have attached the LIG image for reference.
The .hdb file is irrelevant. pdb2gmx is complaining about an H51 atom in your input coordinate file. The file you have loaded in VMD has "G6P instead of “LIG” as the residue name, so you’re using different files. The one you’re providing to pdb2gmx is incorrect.
Dear Justin
thank you for your input.
I have edited the hdb file according to your suggestions as follows:-
G6P 3
1 2 H7 O1 C1 C2
1 2 H8 O2 C2 C1
1 2 H9 O3 C3 C2
1 2 H10 O4 C4 C5
1 5 H C1 O1 C2 O5
1 5 H1 C2 O2 C3 C1
1 5 H2 C3 O3 C4 C2
1 5 H3 C4 O4 C5 C3
1 5 H4 C5 O5 C6 C4
2 6 H6 C6 C5 O6
I got topology but still not sure either it is correct or otherwise. Earlier I was getting a structure crash because of the topology problem.
I have few confusions if you could please help me in understanding this.
As per gromacs manual,
first-line should be number of H atoms added, (# additions) I have to add in total 11 H atoms, but I get the following error while putting 11.
Fatal error:
wrong format in input file ./amber99sb-ildn.ff/G6P.hdb on line
It is also mentioned in the manual that in first-line after residue name " the number of kinds of hydrogen atoms that may be added to this residue by the hydrogen database" I have 3 kinds/environment of H atoms in my ligand, I tried with 3 as well but got same error.
I have 2 H atoms attached to the same C6 atom, If I mention it as below:-
1 6 H61 C6 C5 O6
1 6 H62 C6 C5 O6
Similarly, I used the same names in rtp file but it gives following error:-
atom H611 not found in residue rtp file it seems it is H5.
In manual it is suggested that if two H atoms are attached to the same atom they should be named as “For example, adding two hydrogen atoms to ND2 (in asparagine), the hydrogen atoms will be named and HD22 and HD21”
Please correct me where I am wrong.
I would be really grateful.
Thanks in advance.
Sadaf
The number specified is how many lines of H additions pdb2gmx should read. You have 10 lines (10 types of H additions to make). So change G6P 3 to G6P 10.
This will assign to H atoms to the exact same coordinates. The approach shown above with
