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 Tue Feb 20 2024 - 11:00:02 PST
