VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Oct 26 2018 - 14:30:59 CDT

That was my mistake! Thanks indeed
francesco

On Fri, Oct 26, 2018 at 7:06 PM Gumbart, James C <gumbart_at_physics.gatech.edu>
wrote:

> Try CG2O5 instead of CG205?
>
> Best,
> JC
>
> On Oct 26, 2018, at 11:11 AM, Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>
> Please forget about the partial charges, which are still to be fixed.
> fp
> ---------- Forwarded message ---------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Fri, Oct 26, 2018 at 5:09 PM
> Subject: Unknown atom type CG205 with CGenFF by psfgen
> To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>
>
> psfgen (vmd in text mode) reported
>
>> psfgen) applying patch ZAHI to 2 residue(s)
>> psfgen) unknown atom type CG205
>> psfgen) add atom failed in patch ZAHI
>> ERROR: failed to apply patch
>>
> where
>
>> PRES ZAHI 1.449 ! patch for ligand-HSP bonding
>> ! Patch must be 1-HSP and 2-ZPN
>> ! use in patch statement
>> ! follow with AUTOgenerate ANGles DIHEdrals command
>> GROUP !
>> ATOM 2C10 CG311 0.332 !
>> ATOM 2C9 CG314 0.199 !
>> ATOM 2H91 HGA1 0.09 !
>> ATOM 2C8 CG321 0.127 !
>> ATOM 2C7 CG205 0.333 ! CD2--NE2--CE1
>> GROUP ! /
>> ATOM 2CD2 CPH1 0.219 ! C10--C9--C8--C7
>> ATOM 2NE2 NR3 -0.20 ! |
>> ATOM 2CE1 CPH2 0.349 ! H91
>> DELETE ATOM 2H92
>> DELETE ATOM 1HE2
>> BOND 2C9 1NE2
>> IMPR NE2 CD2 CE1 C9
>> IMPR NE2 CE1 CD2 C9
>>
>
> thins C7-enlarged PRES was included into top_all36_cgenff.rtf.
>
> I am unable to correct my mistake because CG205 is defined in
> top_all36_cgenff.rtf
> Grateful for advice
>
> francesco pietra
>
>
>