[gmx-users] I: How to rolled up a polymer chain

marcello cammarata mstaxmarcello at yahoo.it
Mon Sep 22 14:46:09 CEST 2014

 i had checked all the archives, i have read about 100posts in the last 2 month.
Nobody have problem similar to mine.
Problem for me are Two. 
1- instead i am a doctor, i am not able to find the right advice at your site.
2- In your site there is no space for begginer user.

The main pages where i checked are:
Polyethylene (PE) simulations in Gromacs - please!
.rtp File
Force Fields
Adding a Residue to a Force Field
Modifying a force field

But i don't have find any suggestion for my problem.
Is there an other blog, that i can't see.
i have several of problem with Gromacs, 
- in Cygwin it doen't work, i got a "bash" comand
- the topology need a lig parameters.

one more time, below there is my post. I wpould like if you can help me to solve this question, instead i can try to use an othere MD software.

Ing., Ph.D.,


Il Lunedì 22 Settembre 2014 14:20, marcello cammarata <mstaxmarcello at yahoo.it> ha scritto:

My goal, for now, is to model a polimer (nylon-6) chain, and to find the equilibrium position of the chain considering the capacity to be rolled up itself.
I had create a pdb file using Avogadro software, but when i go to gromacs to input the
 data using the function pdb2gmx And indipendently of the force field that i
                          choose i get :that "Residue LIG not found".

How to solve this?

Ing., Ph.D.,

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