Re: [gmx-users] Rhamnose on 53a6

2012-06-11 Thread Justin A. Lemkul
On 6/11/12 6:06 AM, Thales Kronenberger wrote: Have you tryed online servers as http://davapc1.bioch.dundee.ac.uk/prodrg/ or the Acpype (with Amber)? For Gromos parameterization, ATB produces much better results than PRODRG. http://compbio.biosci.uq.edu.au/atb/ Validation is always require

Re: [gmx-users] Rhamnose on 53a6

2012-06-11 Thread Thales Kronenberger
Have you tryed online servers as http://davapc1.bioch.dundee.ac.uk/prodrg/or the Acpype (with Amber)? 2012/6/11 Marc Gordon > Hello again fellow gromacs users. > > I am looking to model a glucose-rhamnose disaccharide using the 53a6 > forcefield. I wanted to take a look at the naming conventions

Re: [gmx-users] Rhamnose on 53a6

2012-06-11 Thread Mark Abraham
On 11/06/2012 6:11 PM, Marc Gordon wrote: Hello again fellow gromacs users. I am looking to model a glucose-rhamnose disaccharide using the 53a6 forcefield. I wanted to take a look at the naming conventions for carbohydrates but I'm battling to find anything in the pdb2gmx force field files.

[gmx-users] Rhamnose on 53a6

2012-06-11 Thread Marc Gordon
Hello again fellow gromacs users. I am looking to model a glucose-rhamnose disaccharide using the 53a6 forcefield. I wanted to take a look at the naming conventions for carbohydrates but I'm battling to find anything in the pdb2gmx force field files. I downloaded a package of force fields from th