Re: [gmx-users] double bond

2013-10-03 Thread Justin Lemkul
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

Re: [gmx-users] double bond

2013-10-03 Thread Ehsan Sadeghi
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

Re: [gmx-users] double bond

2013-10-03 Thread Justin Lemkul
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

[gmx-users] double bond

2013-10-03 Thread Ehsan Sadeghi
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