From: James Starlight (jmsstarlight_at_gmail.com)
Date: Tue Sep 24 2013 - 15:35:09 CDT
also I wounder to know is there any quicker way to exclude ligand from my
system (especially from the generated psf file ?) E.g I'd like to perform
simulation of the apo system starting with the ligand-included complex.
2013/9/24 James Starlight <jmsstarlight_at_gmail.com>
> Thanks for suggestions!
> IS there any easiest way for manual convertion
> to the step5_assembly.xplor_ext.psf ?
> 2013/9/24 Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>
>> 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
>>> 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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