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CHARMM-GUI generated an empty parameter file
#34769 02/03/15 08:45 PM
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Hi,

I'm using CHARMM-GUI to build a membrane for a crystallized protein that have a co-crystallized cholesterol. I did not have any problems with the protein, but CHARMM-GUI generated an empty parameter file for the cholesterol molecule:
"
* Parameters generated by analogy by
* CHARMM General Force Field (CGenFF) program version 0.9.7 beta
*

! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

BONDS

ANGLES

DIHEDRALS

IMPROPERS

END
"
I intend to use these files for namd simulations so I need a proper parameter file. How can I obtain such file?

Thank you!

Re: CHARMM-GUI generated an empty parameter file
PBC #34773 02/04/15 03:03 AM
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Oftentimes in my experience this indicates that all of the necessary parameters are in the main CGENFF parameter files (i.e. the ParamChem server did not need to generate any extra parameters).

Re: CHARMM-GUI generated an empty parameter file
PBC #34774 02/04/15 03:43 AM
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rmv Online Content
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Cholesterol is already included in CHARMM force fields as an extension to the lipid force field.


Rick Venable
computational chemist

Re: CHARMM-GUI generated an empty parameter file
PBC #34791 02/13/15 05:52 PM
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Thank you for your answers.
The cholesterol molecule wasn't recognized as such by CHARMM-GUI, so I added a mol2 file to obtain the topology and parameters for later use.
The CGenFF parameter file seemed to recognize the atom types of the topology file, but they were incomplete in my file (e.g. CG3R in the topology file were CG3RC1 in the parameter file). I tried to complete them manually but ended with errors like:
"
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG3C41 CG3RC1 (ATOMS 80199 80240)

Charm++ fatal error:
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG3C41 CG3RC1 (ATOMS 80199 80240)
"
I will try to add the cholesterol file to my system after using CHARMM-GUI to generate the topology file using VMD instead of CHARMM-GUI.

Re: CHARMM-GUI generated an empty parameter file
PBC #34793 02/13/15 07:04 PM
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Cholesterol is explicitly present as one of the molecules in the CHARMM-GUI bilayer builder, so it is definitely a known molecule.

Note that there can be issues with ligands when importing PDB files, esp. related to the molecule (residue) name.


Rick Venable
computational chemist

Re: CHARMM-GUI generated an empty parameter file
PBC #34794 02/13/15 08:49 PM
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It worked if I change the residue name to CHL1 while being in a different chain that of the protein.
Thank you.


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