Dear users,
I know there are many questions here about the MD of protein/covalent-bound ligands… but I need to do more about some details… I’d appreciate it if anyone could help me!
I obtained the itp/prm files of the cys-ligand properly hydrogenated and included the information in the aminoacids.rtp. However, when I was creating an entry in the aminoacids.hdb file I didn’t understand the organization:
CYS 4
1 1 HN N CA -C
1 5 HA CA C CB N
2 6 HB CB CA SG
1 2 HG1 SG CB CA
What are these numbers in columns 1 and 2? Is column 4 the atom to which hydrogen is bonded while the others are the atoms bonded to it?
The other questions are about the ffbonded.itp.
In the manual, it is shown that " If you require any new bonded types, add them to ffbonded.itp". Since my entire ligand plus the covalent bond are “new bonded types” (at least different from protein), should I include everything in the prm file in the ffbonded.itp (I think the prm is closer to the information that the itp need) or just the information about the covalent bond?
One last question about this itp file. The str file generated by Cgenff does not have the b0 and kb of the bond (cystein)S-(ligand)C (but showed angles and dihedral). How can I get these values? I believe b0 could be the distance in the PDB file, but I think the kb isn’t so simple to find…
The parameters you see listed in the .str file are ones that are new and otherwise not already present in the force field. Every other interaction is already present in the parent force field, meaning you do not need to do anything.
Ok. So, in the example of Cysteine residue, the second line means 1 hydrogen planar HN added, the fourth line added 2 tetrahedral HBs, etc, is that right? One more question. My new Cys-lig residue has 30 hydrogen atoms, must I create 30 lines or (for example) HB2 and HB3 are bonded to the same CB atom, can I add a line 2 (atoms) 6 (two tetrahedral hydrogens) HB CB .... (H1 and H3 are bounded to the same C5: 2 6 H C5...)?
OK. I have nothing to do with the S-C… but I need to introduce all other parameters present in the .str (.prm) file in the ffbonded.itp, is that right?
Not necessarily 30 lines, but note that GROMACS will start numbering from 1, so you will not generate HB2 and HB3, you will generate HB1 and HB2. If you have atoms H1 and H3 bonded to a single atom, those have to be specified with individual lines, not 2 at once (because you’ll get H1 and H2, not H3).
Hum… I don’t know if I understood it…
So do I have to change the numbering in the .rtp file (e.g. HB2 to HB1) or doesn’t it matter (and it is only something for GROMACS)?
You will make your life easier if you adopt the numbering convention in GROMACS. Here is an example.
2 6 HB CB CA CG
This generates 2 HB atoms (HB1 and HB2) in a tetrahedral configuration around CB. If you want to generate two atoms named H1 and H3 bonded to CB in the same geometry, you would have to do something like:
1 6 H1 CB CA CG
1 6 H3 CB CG CA
Note the inversion of the last two control atoms to invert the stereochemistry of the added H, otherwise they will be added on top of one another and you’ll have an infinite force during minimization.
Everything looks like to be working fine up to now…
I want to ask 2 more questions:
What should I include in the aminoacids.rtp file [ improper ] and [ cmap ]? Could I maintain the normal lines that were in the DCYS plus the lines in .prm file?
[ impropers ]
N -C CA H
C CA +N O
C3 C2 N5 SG
C21 C22 N4 O4
[ cmap ]
-C N CA C +N
How can I include the peptide bond of the new residue (Cys+lig) with the rest of the protein? Is it only include the line C +N, as follows?
Besides, since C1, N1, etc are not atoms in the residues by default, should I include these atoms in the ffnonbonded.itp? If yes, how can I get the sigma and epsilon values?
OK.
I test here and I got 3 warning/error messages after running grompp:
It shows the following message for all the new types (except hydrogen atoms). What should I do? Should I rename the types (in ffbonded and aminoacids.rtp) or search for the types in the ffbonded and see if the bonds/angles/dihedrals are already present (deleting the new ones)?
WARNING 1 [file ffnonbonded.itp, line 449]:
Atomtype NG321 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
It showed this error. Reading the ffnonbonded.itp, the line shows OG2D1 8 15.999000 0.000 A and does not have the sigma and epsilon values. Is there a way to fix it? OG2D1 is the type for all C=O oxygen atoms
WARNING 4 [file ffnonbonded.itp, line 452]:
Too few parameters on line (source file
/home/xavie/gromacs-2021.3/src/gromacs/gmxpreprocess/toppush.cpp, line
343)
It shows the following error for all the bonds, angles, and dihedrals related to the atoms in the peptide bond. How can I fix it (I added the line C +N in [ bonds ] of the aminoacids.rtp file)?
ERROR 1 [file topol.top, line 7344]:
No default Bond types
ERROR 3 [file topol.top, line 26428]:
No default U-B types
ERROR 11 [file topol.top, line 36974]:
No default Proper Dih. types
ERROR 31 [file topol.top, line 44106]:
No default Improper Dih. types
ERROR 33 [file topol.top, line 44702]:
Unknown cmap torsion between atoms 2221 2223 2225 2232 2234
You should never have to mess with anything in [atomtypes] in the force field files. The duplicate definition means you already have the N type that you need so you shouldn’t be adding it again. A misformatted line means you added an incomplete line.
As for the missing parameters, I can’t say anything about them without knowing what those parameters are and if they were added to your original .str file as new parameters. The CMAP torsions won’t be; you’ll have to add those by analogy because the backbone doesn’t differ among most amino acids (only Gly and Pro are different).
How can I do this? I ask because I didn’t change the ffnonbonded.itp. So, I didn’t include these atomtypes. The forcefield files I’ve changed were aminoacids.hbd, aminoacids.rtp and ffbonded.itp (I copied all lines in .prm file and pasted them here).
You said, change the -N from NG321 to NH1, CA from CG311 to CTD1, etc?
Something isn’t adding up but without access to your files, I can’t tell what. The complaint is about multiply defined atom types so I can’t see how else you would be getting that unless you have an #include statement somewhere else that’s causing the problem.
To solve the CMAP issue, you would just copy the standard CMAP entry for the canonical protein atom types and use the CGenFF atom types.
Dear @jalemkul
I changed the [ atomtypes ] of the cysteine residue in the cys-lig (CSL) to those in the DCYS, maintaining the CGenFF ones in the ligand. Instead of 34 errors related to the atoms in the cys backbone, it showed 10 errors:
WARNING 1 [file ffbonded.itp, line 6991]:
Bondtype U-B was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
old: 110 365.682 0 0 110 365.682 0 0
new: NH1 CTD1 C 5 107.000000 418.400000 0.00000000 0.00
ERROR 1 [file ffbonded.itp, line 21554]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
ERROR 2 [file ffbonded.itp, line 21594]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
ERROR 3 [file ffbonded.itp, line 21662]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
ERROR 4 [file ffbonded.itp, line 21666]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 117432 of the 167910 1-4 parameter combinations
ERROR 5 [file topol.top, line 7355]:
No default Bond types
ERROR 6 [file topol.top, line 26465]:
No default U-B types
ERROR 7 [file topol.top, line 37012]:
No default Proper Dih. types
ERROR 8 [file topol.top, line 37013]:
No default Proper Dih. types
ERROR 9 [file topol.top, line 37014]:
No default Proper Dih. types
ERROR 10 [file topol.top, line 37015]:
No default Proper Dih. types
Is there a problem doing this?
The errors 1-4 are related to the atoms in the cysteine backbone. Could I solve it by putting the correspondent line below the actual line? For example:
NH1 CTD1 C O … mult 4
NH1 CTD1 C O … mult 5 (the new one)
The errors 5-10 are related to the new bond Cys(S)-Lig(C).
I made some more changes in the files, and I got less error messages:
WARNING 1 [file ffbonded.itp, line 6991]:
Bondtype U-B was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
old: 110 365.682 0 0 110 365.682 0 0
new: NH1 CTD1 C 5 107.000000 418.400000 0.00000000 0.00
ERROR 1 [file ffbonded.itp, line 21662]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
ERROR 2 [file ffbonded.itp, line 21666]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 117432 of the 167910 1-4 parameter combinations
ERROR 3 [file topol.top, line 7355]:
No default Bond types
ERROR 4 [file topol.top, line 26465]:
No default U-B types
but the questions continue…
Is there a problem changing the [ atomtypes ] to cysteine types?
Can I solve the errors 1 and 2 by putting the correspondent line below the actual line? For example:
NH1 CTD1 C O … mult 4
NH1 CTD1 C O … mult 5 (the new one)
How can I solve the errors 3-4 since they are related to the new bond Cys(S)-Lig(C)?
The files are in the same shared folder: Here are the modified files