From: James Starlight (jmsstarlight_at_gmail.com)
Date: Tue Sep 24 2013 - 09:38:30 CDT
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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