It looks like we faced very similar situations, Amy, that is exactly what I was trying to do. After much frustration and deliberation, I decided to give up on using the CHARMM parameters for the ligand. For anyone facing similar issues in the future, I ended up using antechamber to generate parameters in GAFF2, then combined these parameters with the entire system pdb and the OL3 forcefield for the RNA (make sure to change the atom and residue names to match those used by amber) in tleap to produce the .prmtop and rst7 file following this tutorial (
https://ambermd.org/tutorials/basic/tutorial4b/). Thanks for the assistance Amy.
Collin
________________________________
From: He, Amy <he.1768.buckeyemail.osu.edu>
Sent: Tuesday, February 20, 2024 8:54 PM
To: Collin Nisler <cnisler.uchicago.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Converting CGenFF CHARMM parameters in tleap
Hi Collin,
I’m not sure if I’m making good advice here.. in the Python API, it’s possible to override the strictly supported types and generate the reusable files, but I’m not entirely sure if they are strictly correct. I actually asked very similar things before. Eventually I didn’t use CGENFF in my work because my base force field for the rest of my system is Amber.
Out of curiosity, is your base force field CHARMM, or are you trying to embed these modifications to an existing Amber force field?
Something like this:
import parmed
from parmed import gromacs, amber
# I started with a gmx top file with CGENFF parameters
gmx_top = gromacs.GromacsTopologyFile("/Users/amyhe/Downloads/6c8e_eq1_h/6c8e_eq1_h_gmx.top")
chamber_prm = amber.ChamberParm.from_structure(gmx_top)
chamber_prm.write_parm("/Users/amyhe/Downloads/6c8e_eq1_h/6c8e_eq1_h_chamber.prmtop")
#amb = amber.AmberFormat("/Users/amyhe/Downloads/6c8e_eq1_h/6c8e_eq1_h_chamber.mdl")
#amb.write_parm("/Users/amyhe/Downloads/6c8e_eq1_h/6c8e_eq1_h_chamber.prmtop")
# start here if you have prmtop
eq1 = parmed.load_file('/Users/amyhe/Downloads/6c8e_eq1_h/6c8e_eq1_h_chamber.prmtop', \
xyz='/Users/amyhe/Downloads/6c8e_eq1_h/6c8e_eq1_h_gmx.pdb')
from parmed.tools.actions import writeFrcmod,writeOFF
writeOFF.strictly_supported = (amber.AmberParm, amber.ChamberParm)
writer = writeOFF(eq1, '/Users/amyhe/Downloads/6c8e_eq1_h/6c8e_eq1_h_chamber.lib')
writer.execute()
writeFrcmod.strictly_supported = (amber.AmberParm, amber.ChamberParm)
writer = writeFrcmod(eq1, '/Users/amyhe/Downloads/6c8e_eq1_h/6c8e_eq1_h_chamber.frcmod')
writer.execute()
Generates some (maybe not entirely correct!) OFF lib file and frcmod file. Again I’m really not sure if I’m doing the right thing. More experienced users and devs on this mailing list, please help us…
Bests,
Amy
From: Collin Nisler <cnisler.uchicago.edu>
Date: Tuesday, February 20, 2024 at 5:36 PM
To: He, Amy <he.1768.buckeyemail.osu.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: Converting CGenFF CHARMM parameters in tleap
Thanks Amy, I didn't notice before that chamber has a writeFrcmod command. Unfortunately, when I attempt to do this I get the error: ChamberParm objects are not supported by this action And when I search, this has been discussed before here
Thanks Amy, I didn't notice before that chamber has a writeFrcmod command. Unfortunately, when I attempt to do this I get the error:
ChamberParm objects are not supported by this action
And when I search, this has been discussed before here (
http://archive.ambermd.org/201902/0177.html<
https://urldefense.com/v3/__http:/archive.ambermd.org/201902/0177.html__;!!KGKeukY!3ltJwQxIQFXC_8Np59eqZy2Dz7j1RG9av3Ifkg-1V9NDTi_UTER9_Xq-VTjyHgSaCk4HY-BWJQ2xZ9fIINTABz8WNe_sdWFO$>). Apparently, it is possible to go from CHARMM to .prmtop, but there is no way currently to express parameters originally from a CHARMM format to a frcmod. Is there any other approach I could try to combine CHARMM derived parameters for a ligand with standard OL3 parameters for the RNA duplex in a single system? I am really trying to avoid using GAFF for this.
Collin
________________________________
From: He, Amy <he.1768.buckeyemail.osu.edu>
Sent: Tuesday, February 20, 2024 3:43 PM
To: Collin Nisler <cnisler.uchicago.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Converting CGenFF CHARMM parameters in tleap
Hi Collin,
I was under the impression that
“loadamberparams” only read Amber frcmod/parm.dat files.
In addition to .frcmod, typical reusable file formats for nonstandard residues are:
OFF Library files (.lib) or Prep input files (.prepi).
If you wish to write these reusable Amber parameter files from the CHARMM files, the ParmEd program might be helpful. You can find more information on ParmEd in the recent Amber Manual or from the documentation site:
https://parmed.github.io/ParmEd/html/index.html<
https://urldefense.com/v3/__https:/parmed.github.io/ParmEd/html/index.html__;!!KGKeukY!3ltJwQxIQFXC_8Np59eqZy2Dz7j1RG9av3Ifkg-1V9NDTi_UTER9_Xq-VTjyHgSaCk4HY-BWJQ2xZ9fIINTABz8WNfgS_SDX$>
The parameter/topology (.prmtop) files may not be reusable in tleap, but it could be one input for ParmEd.
--
Amy He
Hadad Lab . OSU
He.1768.osu.edu
From: Collin Nisler via AMBER <amber.ambermd.org>
Date: Tuesday, February 20, 2024 at 1:48 PM
To: Collin Nisler via AMBER <amber.ambermd.org>
Subject: [AMBER] Converting CGenFF CHARMM parameters in tleap
Hello, I am attempting to build an RNA system in tleap that contains a nonstandard residue, in addition to a standard RNA duplex. I have CHARMM parameters and a psf file for the nonstandard residue, and have created a separate .prmtop and mol2 file for this residue. I am having difficulties creating a solvated system with .crd and .prmtop files for the entire system using tleap. I load the .prmtop into tleap using the "loadamberparams" command, and get the following messages:
Warning: %FLAG: mass not read - omitting
Warning: %FORMAT(20a4): mass not read - omitting
Warning: Incomplete Angle line:
%FLAG HBOND_BCOEF
Warning: Incomplete Improper Torsion line:
%FLAG HBCUT
When I then attempt to solvate the system, I get the following message for each atom in the nonstandard residue:
(using default radius 1.500000 for P1)
Then finally, when I attempt to output the files from tleap, I get the following error for each atom:
Error: For atom (.R<EQ1 1>.A<P1 1>) could not find vdW (or other) parameters for type (P1)
I am new to Amber, but I have tried to familiarize myself with the file formats and as far as I can tell, all the parameters are present in the .prmtop file generated for the nonstandard residue that I load into tleap. Is tleap just not meant to read .prmtop files, and if so how else could I go about converting CHARMM parameters generated from CGenFF to Amber format? Thanks very much for any help.
Collin
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Received on Wed Feb 21 2024 - 12:30:02 PST
