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

varsha gautham varsha.gautham88 at gmail.com
Tue Feb 3 12:28:29 CET 2009

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.

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.

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