[gmx-users] constructing polymer.itp files from monomer files obtained from prodrg server

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 3 12:35:34 CET 2009

varsha gautham wrote:
> Dear all,
> Am trying for a simulation with polymers on a lipid bilayer.when i give 
> the entire polymer file which consists of 228 atoms to prodrg server for 
> generating itp files its taking only a block of polymer as input and 
> generating itp files for that polymer alone.I have two different monomer 
> units in my system.I tried to generate itp files for these two separetly 
> and included that in my top file.The thing is it is ,considering them as 
> two separate sytem so that connectivity between these two are missing 
> in  the bonded information .
> Is there anyway to get a topology files for entire system?i tried using 
> usual commands by including in rtp entries..but thats not helpful.Please 
> give me a detailed solution on this.

Making an .rtp entry is the way to go with polymer building blocks.  Saying that 
rtp entries were "not helpful" is not a useful way to get advice, aside from 
"read Chapter 5 more thoroughly."  What have you tried?  What problems did you 


> I have a psf  files in hand for that polymer.how to convert a psf file 
> to top file..are there any scripts available.
> Please let me know in detail about this.Thanks in advance.
> -varsha
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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