VMD-L Mailing List

From: Reinke.Patrick_at_mh-hannover.de
Date: Mon Aug 26 2019 - 10:13:01 CDT

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