Hi Amber Community,
I am trying to use CHAMBER to generate an AMBER ParmTop file for a simple RNA duplex (1RNA.pdb). I have performed multiple tests to try and detect where CHAMBER fails. Here is my working protocol of what produced a ParmTop file and what didn't (along with relevant error messages). For the record, I am coming from using CHARMM so the CRD and PSF (regular, non-XPLOR format) files are generated via CHARMM and I am using an unmodified top_all27_na.rtf (topology file) and par_all27_na.prm (parameter file). I understand that there are CHARMM36 topology and parameter files but I figured that I should try to get this to work first before moving ahead. My goal is to generate the ParmTop file so that I can run simulations of RNA using PMEMD with the CHARMM force field.
1) Starting with 1RNA.pdb, this structure was processed through CHARMM and all missing atoms were added. The CRD and PSF files were generated (no waters, no ions) using the CHARMM parameter and topology files mentioned above.
2) The following CHAMBER command was used to try and generate a ParmTop file for 1RNA:
chamber -top top_all27_na.rtf -param par_all27_na.prm -psf 1rna.psf -crd 1rna.crd -nocmap -p prmtop
However, this fails with the following error:
--- Found all ATOM TYPES in topology file
--- Found all nonbond parametersAt line 584 of file _psfprm.fFortran runtime error: Bad value during floating point read
A Google search with different queries didn't seem to bring up any suggestions as to how to resolve this and I wanted to make sure that I wasn't doing something wrong so I tried simpler tests
3) I used CHAMBER to test out a small metenkephalin peptide (note that the parameter and topology files are different in this case because it is a protein):
chamber -top top_all27_prot.rtf -param par_all27_prot.prm -psf met.psf -crd met.crd -nocmap -p prmtop
This simple case produced a ParmTop file.
4) Next, I tried a DNA duplex (1bna.pdb) thinking that it was somehow a problem with RNA. However, I get the same error as the RNA above.
--- Found all ATOM TYPES in topology file
--- Found all nonbond parametersAt line 845 of file _psfprm.fFortran runtime error: Bad value during floating point read
This time, the line is 845 rather than 584. It is unclear if this is referring to a line in psfprm.f or in one of the input files (CRD, PSF, parmater, topology,etc??). Any clarification would be greatly appreciated.
5) Finally, I simplified the RNA system so that it contained either a single URACIL residue or a single ADENINE residue:
chamber -top top_all27_na.rtf -param par_all27_na.prm -psf URA.psf -crd URA.crd -nocmap -p prmtop
chamber -top top_all27_na.rtf -param par_all27_na.prm -psf ADE.psf -crd ADE.crd -nocmap -p prmtop
In both cases, a ParmTop file is produced successfully.
6) I move to a di-nucleotide (two residues) of URA-ADE:
chamber -top top_all27_na.rtf -param par_all27_na.prm -psf UA.psf -crd UA.crd -nocmap -p prmtop
Again, this two nucleotide system produces the same error as the DNA case:
--- Found all ATOM TYPES in topology file
--- Found all nonbond parametersAt line 845 of file _psfprm.fFortran runtime error: Bad value during floating point read
A di-nucleotide of DNA also produces this identical error.
This is as far as I have reached without digging into the CHAMBER source code so any suggestions, comments, or hints would be greatly appreciated.
Thank you for your time.
Sean
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Received on Thu May 03 2012 - 08:30:02 PDT
