VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Aug 26 2019 - 19:26:17 CDT

Dear Patrick,
Because the ACE is defined as a patch, not a residue of its own, the
correct way to handle this is to not have the ACE residue in your input
file, but rather, specify ACE as the N-terminal patch for your protein
chain of interest. This can be done in the autopsf GUI using the "Chains
Identified" section of the menu.
Best,
Peter

On Mon, Aug 26, 2019 at 12:37 PM <Reinke.Patrick_at_mh-hannover.de> wrote:

> Dear VMD board reader,
>
> I want to create a PSF file with the VMD AutoPSF plugin. I have an
> acetylated protein. The acetylation is named ACE in my PDB-file:
> ...
> MODEL 1
> ATOM 1 CH3 ACE C 1 -61.666 70.029 95.938 1.00
> 20.00 C
> ATOM 2 C ACE C 1 -63.170 70.100 95.789 1.00
> 20.00 C
> ATOM 3 O ACE C 1 -63.867 69.207 96.159 1.00
> 20.00 O
> ATOM 4 HH31 ACE C 1 -61.218 70.940 95.541 1.00
> 0.00 H
> ATOM 5 HH32 ACE C 1 -61.409 69.928 96.993 1.00
> 0.00 H
> ATOM 6 HH33 ACE C 1 -61.286 69.168 95.388 1.00
> 0.00 H
> ATOM 7 N MET C 2 -63.645 71.245 95.209 1.00
> 73.93 N
> ATOM 8 CA MET C 2 -65.061 71.459 94.999 1.00
> 95.46 C
> ...
>
> After Loading the Topology files of CHARMM36 into AutoPSF, I use the
> "Guess and split chains using current selections" command of step 2. The
> Segmends in the "Step 3: Segments Identified" field looks like this:
>
> CP1 160 1- 2638 NTER CTER Prot
> DP1 161 2639-5276 NTER CTER Prot
> CO1 1 5277-5282 none none Water
> DO1 1 5283-5287 none none Water
>
> Whereas the CO1 and DO1 represent my acetyl-group. When I press "create
> chains" an error pops up:
>
> error: failed on end of segment
> details:
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> while executing
> "segment $segid {
> pdb $segfile
>
> When I look in the console this additoinal error appears:
> psfgen) Info: generating structure...psfgen) unknown residue type ACE
> failed!
>
> I use the CHARMM36 top_*.rtf files, where ACE is defined (as PRES). I
> looked for old board entrys (there are some for N-terminal acetylation, but
> none is helpful to my error) and the AutoPSF guide did not help me either
> (I am no expert, I have to admit).
>
> Greetings and best regards,
> Patrick
>
>
> * --*
> * Patrick Reinke*
> *Medizinische Hochschule Hannover*
>
> *Institut für Biophysikalische Chemie *OE4350,Carl-Neuberg-Str. 1,
> D-30625 Hannover
> Tel.: +49(0)511-532-5177
> reinke.patrick_at_mh-hannover.de
> www.mh-hannover.de
>
>