[gmx-users] guanidinium in water

[Justin Lemkul]

Please don't spam the list with repeated pleas for help.  Realize that this is 
an international mailing list with hundreds (or more) subscribers who give of 
their free time to help.  I'm not going to be able to instantly answer all of 
your emails within minutes.  I'll answer this most recent one with whatever 
information I can.

On 4/27/14, 1:02 PM, Swetha Srinivasan wrote:
> Hi Lemkul,
>
> How do I correct this.Could you please help me?
>

The error is in the topology.  You still haven't given any evidence of how you 
made it, why you're using this type of interaction, or what atoms it applies to. 
  Hint: post the content of the topology.

If you don't know what a topology is, you should stop what you're doing 
immediately and work through as many tutorials as you can find.  Time spent 
learning proper techniques will save you potentially months of wasted work based 
on whatever you might have done incorrectly.

To create a mixture of guanidinium in water, you can follow the protocol 
described here: http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents. 
It's a very standard thing to do.  Constructing the system is the easy part; 
defining the topology is a much harder thing to do, though guanidinium should 
have a fairly easily defined topology since it is part of the Arg side chain.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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