From: Behrmann, Elmar (Elmar.Behrmann_at_charite.de)
Date: Wed Oct 16 2013 - 07:36:12 CDT

Dear all,

I am trying to use the Dowser-plugin of VMD to solvate a GC-rich RNA-loop structure. While I am able to use dower_gui --> 'Process input structure', a subsequent call to Dowser fails with 'child process exited abnormally'. When trying to run Dowser by hand on the pdb prepared by VMD, I realized that the reformatPDB module of Dowser appears to have problems with my guanines (both G and 5-prime G5) while cytosines and my 3-prime adenine (A3) seem to be fine:
REMARK ERROR: Residue type G5 not found in the type dictionary
REMARK ERROR: Residue type G not found in the type dictionary
REMARK ERROR: Residue type G not found in the type dictionary
REMARK ERROR: Residue type G not found in the type dictionary
REMARK ERROR: Residue type G not found in the type dictionary
REMARK ERROR: Residue type G not found in the type dictionary
REMARK ERROR: Residue type G not found in the type dictionary
REMARK ERROR: Residue type G not found in the type dictionary
*** execution of dowser is terminated

Comparing the pdb and the rna atomtypes dictionary (http://www.ks.uiuc.edu/Research/vmd/plugins/dowser/dowser-rna.html) did not reveal any obvious mismatches to me. Has anybody ever encountered a similar problem and perhaps knows a workaround?

best regards,
Elmar

--------------------------------------------------------------
Dr. rer. nat. Elmar Behrmann

Charité - Institute of Medical Physics and Biophysics
Charitéplatz 1
Intern: Virchowweg 6 / Gebäude 2360 / E3 R320
10117 Berlin

tel.: office +(49)30-450-524 187
tel.: lab +(49)30-450-524 167
fax: +(49)30-450-524 952

e-mail: elmar.behrmann_at_charite.de<mailto:elmar.behrmann_at_charite.de>