VMD-L Mailing List

From: Gumbart, James C (gumbart_at_physics.gatech.edu)
Date: Fri Oct 26 2018 - 12:06:15 CDT

Try CG2O5 instead of CG205?

Best,
JC

On Oct 26, 2018, at 11:11 AM, Francesco Pietra <chiendarret_at_gmail.com<mailto: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<mailto: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<mailto: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