[gmx-users] Solvation Free energy using Amber

[jorge_quintero at ciencias.uis.edu.co]

Ok, thank you for your time.

>
>
> jorge_quintero at ciencias.uis.edu.co wrote:
>> Ok Justin, I send You a copy of muy simulation for SFE with two proteins
>> +
>> water.  Look the top file structure.  Thanks again.
>>
>
> A quick look at the topologies indicates to me that something is badly
> broken.
> The net charge on each of your protein subunits is 2.505 in state A, which
> is
> obviously wrong.  In addition, each subunit .itp file defines the molecule
> as
> Protein_A, which is also wrong, if you should have Protein_A and
> Protein_B.
>
> Besides that, I don't feel the desire to do your work for you in terms of
> troubleshooting.  If you want advice on the errors you're seeing, post the
> error
> messages, as I said before.  Everyone on this list has his/her own work to
> be
> doing, and we're not asking to do yours as well.  If you want free help,
> make it
> easy for the people from whom you're asking it. :)
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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