[gmx-users] C instead of CH2 in alkane chain with PRODRG

Justin Lemkul jalemkul at vt.edu
Fri Feb 1 20:09:52 CET 2013

On 2/1/13 11:47 AM, Stephan Gekle wrote:
> Dear all,
> I want to produce a perylene with a connected alkane chain using PRODRG. I draw the molecule using JME, run it through PRODRG. Then some of the polar hydrogens connected to the C rings are missing. But the alkane chains have the correct united atom type (CH2/CH3).
> Following another post, I then take the PDB file, repost into PRODRG, use the ADDHYD command to add hydrogens to the C ring atoms where I want explicit H's and run it through PRODRG.
> In the result, the desired H's are there, but the CH2/CH3 of the alkane chain have turned into plain Cs! And there are no explicit hydrogens connected to the alkane chains, either.
> Any hints how to solve this would be greatly appreciated!

Works fine for me using JME.  I find that when uploading a .pdb file, all 
hydrogens should be present.  Sometimes I think it misinterprets hybridization 
state without them.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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