I am running the pdb2gmx command for my protein using Gromos 54a7 force field, but I have this error:
Fatal error:
Atom type OUrea (residue UREA) not found in atomtype database
while this atom type (OUrea) is in my ffnonbonded.itp file !!!!
what shall I do to solve this error???
Thanks
1. Verify the presence of the OUrea atom type in the ffnonbonded.itp file: Open the ffnonbonded.itp file associated with the Gromos 54a7 force field and check if the OUrea atom type is indeed defined. Ensure that the spelling, capitalization, and any special characters match exactly with the error message you received.
2. Confirm the correct inclusion of the force field files: Ensure that you have correctly included and referenced the Gromos 54a7 force field files in your simulation setup. Double-check the file paths and names to make sure they are accurate.
3. Check for any custom modifications: If you have made custom modifications to the force field or created your own atom type, ensure that the changes are reflected consistently throughout the ffnonbonded.itp file and other related force field parameter files.
4. Examine the residue topology file: Check the topology file (.top) associated with your protein. Ensure that the UREA residue is defined correctly, including the atom names and types. Verify that the UREA residue is properly connected and specified in the .top file.
5. Ensure proper force field selection: When running the pdb2gmx command, make sure you are explicitly specifying the Gromos 54a7 force field option, such as "-ff gromos54a7" or a similar flag depending on your specific software package.
Thank you dear Farshad for your response,
The OUrea atom type is located in my ffnonbonded.itp file and the OUrea atom type do not exist in my protein.
actually I have added a hydroxyl group to the Proline aminoacid in my protein and because of that I have defined the 3-hydroxyproline in my aminoacids.rtp file from Gromos54a7 folder (I have copied the Gromos54a7 folder to my working directory):
This is what I have added to the end of aminoacids.rtp file:
; 3-hydroxyproline (R)
[ PH3 ]
[ atoms ]
N N 0.00000 0
CA CH1 0.00000 1
CB CH1 0.26600 2
OG1 OA -0.67400 2
HG1 H 0.40800 2
CG2 CH2R 0.00000 3
CD CH2R 0.00000 3
C C 0.450 4
O O -0.450 4
[ bonds ]
N CA gb_21
N CD gb_21
CA CB gb_27
CA C gb_27
CB OG1 gb_18
CB CG2 gb_27
OG1 HG1 gb_1
CG2 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 OG1 ga_13
CA CB CG2 ga_13
OG1 CB CG2 ga_13
CB OG1 HG1 ga_12
CB CG2 CD ga_13
N CD CG2 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
CB CG2 CA OG1 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_44
-C N CA C gd_43
CA N CD CG2 gd_39
N CA CB CG2 gd_34
N CA C +N gd_45
N CA C +N gd_42
CA CB OG1 HG1 gd_23
CA CB CG2 CD gd_34
CB CG2 CD N gd_34
besides I have defined the 3-hydroxyproline in the residuetypes.dat file.
maybe this error is because of these changes????
How I could solve it???
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