[Chimera-users] Parse error Chimera

[Dorfner, Maja]

To whom it may concern,

Using Swissmodel, I have constructed a model based on an original PDB 
file.
NAP is part of this model. The docking works when the option of either 
"Ignore chains of non-standart residues" or "Ignore all non-standart 
residues" is chosen as false. The Problem is that in the PDBQT file of 
the receptor shows that NAP was not considered during the docking, 
making the Substrate float either within the NAP or to far from it. The 
docking worked fine with the original PDB file but not with the newly 
modeled one.

Could the problem be that the NAP is a separate chain?
I have already tried to erase the H before using AutoDock Vina.

Here is the Reply log:
Running AutoDock Vina for PmWT.pdb failed; see Reply Log for more 
information

Application stderr
-----


Parse error on line 3578 in file "receptor.pdbqt": ATOM syntax 
incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom 
types are case-sensitive.
-----
Application stdout
-----
#################################################################
# If you used AutoDock Vina in your work, please cite:          #
#                                                               #
# O. Trott, A. J. Olson,                                        #
# AutoDock Vina: improving the speed and accuracy of docking    #
# with a new scoring function, efficient optimization and       #
# multithreading, Journal of Computational Chemistry 31 (2010)  #
# 455-461                                                       #
#                                                               #
# DOI 10.1002/jcc.21334                                         #
#                                                               #
# Please see http://vina.scripps.edu for more information.      #
#################################################################

Detected 4 CPUs
Reading input ... -----

Thank you for your patience.

Sincerely,
Maja Dorfner