From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Sep 24 2013 - 10:54:37 CDT
On 09/24/2013 10:38 AM, James Starlight wrote:
> 1) I've done parametrization of the ligand with the CGENff
> This is my output
> http://www.charmm-gui.org/?doc=input/micelle&time=1380010382
>
> now when I try to launch equilibration using charm-gui inp files
>
> I've obtain error
>
> Charm++ fatal error:
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG31
>
> I've noticed that my ligand has atom CG311 (not CG31) and that atom is
> present in the cgenff.prm which are included in the inp file. So How I
> could fix it?
The CHARMM carbohydrate FF and CGenFF only work in "extended format".
step1_pdbreader.inp generates an extended psf file (
step1_pdbreader.xplor_ext.psf ) but step5_assembly.xplor.psf doesn't. One
could consider this a shortcoming in CHARMM-GUI (hint, hint). As a
workaround, if you have access to CHARMM, you could make the following
change to step5_assembly.inp and run it again:
< ioformat noext
-- > ioformat ext > 2) I've tried to parametrize my complexes using antechamber with explicit > charge definition (all my ligands have +1 charge) but in all cases I've > obtained error > > CHARMM> read para flex card unit 20 append > > PARAMETER FILE BEING READ FROM UNIT 20 > TITLE> * FORCE FIELD PARAMETER FILE. > TITLE> * > > ***** LEVEL -1 WARNING FROM ***** > ***** ATOM already exists with a different name > ****************************************** > BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5 > > I've checked mol2 file (generated by chimera) and didndt obtan any errors > in it. What are the reason of that error? I don't know, but one thing I can tell you is that you shoudn't mix an AMBER ligand with a CHARMM protein. To get balanced interactions, your system either has to be all-AMBER or all-CHARMM.
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