From: Sunhwan Jo (sunhwan_at_uchicago.edu)
Date: Tue Sep 24 2013 - 10:34:40 CDT
James,
It appears to be a CHARMM-GUI bug.
1) CG311 is recognized as CG31 because CHARMM-GUI didn't write extended PSF format. In addition, step6.1 input also didn't read ligand's parameter file. I have submitted the patch to our source repository. It may takes sometime it gets updated to the main website. In the meantime, you can use the following psf
https://dl.dropboxusercontent.com/u/163146/step5_assembly.psf
And add following line in your input:
parameters ../lig/lig.prm
2) I'm not sure what is the cause. I'll have to relay this to other developer and see what she thinks.
Best,
Sunhwan
On Sep 24, 2013, at 9:38 AM, James Starlight <jmsstarlight_at_gmail.com<mailto:jmsstarlight_at_gmail.com>>
wrote:
Dear Namd users!
I've forced with the problems during preparation of the membrane receptor-ligand complex embedded into the micelle.
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?
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?
JAmes
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