On 10/3/13 4:15 PM, Ehsan Sadeghi wrote:
Thanks Justin. I will try different bond parameters. I usually use PyMol or
Chimera for visualization. Do you have any recommendation for a visualization
software?
For quick visualization, VMD (but it often gets bonds wrong if they are not in
line
t: Thursday, October 3, 2013 1:09:05 PM
Subject: Re: [gmx-users] double bond
On 10/3/13 3:08 PM, Ehsan Sadeghi wrote:
> Hi gromacs users,
>
> In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2
> double bonds with 2 O, 1 single bond with another O, and i sing
On 10/3/13 3:08 PM, Ehsan Sadeghi wrote:
Hi gromacs users,
In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double
bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6
bonds). When I do energy minimization in vacuum, I got two F atoms nonbon
Hi gromacs users,
In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double
bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6
bonds). When I do energy minimization in vacuum, I got two F atoms nonbonded to
my C atom. I think, gromacs generate
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