[gmx-users] trouble minimizing structure with mdrun

[Tsjerk Wassenaar]

Hi Jack,

> On Mon, Jan 4, 2010 at 2:44 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>> Hi Jack,
>>

<snip>

>> After preparation with (V|NA)MD, did pdb2gmx correctly assign chains,
>> or did it tie chains together? In the latter case it would have issued
>> a number of "Long Bond Warnings". Did anything else odd show up in
>> the output of any of those steps? Did you actually read through it?

Post pdb2gmx/grompp output to help us help you.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist