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

Stephan Gekle stephan.gekle at uni-bayreuth.de
Fri Feb 1 17:47:52 CET 2013

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!

Thanks a lot in advance,


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