Re: [gmx-users] Dangling bond at terminal end of RNA rosetta model

2012-12-26 Thread Mark Abraham
On Thu, Dec 27, 2012 at 12:32 AM, Gert Peters wrote: > Hi everybody, > > Im trying to use GROMACS for MD of a RNA model generated by Rosetta > (FARFAR). As a test I try processing a modelledpdb file. When I prepare > thetopology files (pdb2gmx -f test.pdb -ff amber99 -ignh > ) from pdb I encounte

Re: [gmx-users] Dangling bond at terminal end of RNA rosetta model

2012-12-26 Thread Justin Lemkul
On 12/26/12 6:32 PM, Gert Peters wrote: Hi everybody, Im trying to use GROMACS for MD of a RNA model generated by Rosetta (FARFAR). As a test I try processing a modelledpdb file. When I prepare thetopology files (pdb2gmx -f test.pdb -ff amber99 -ignh ) from pdb I encounter following output :

[gmx-users] Dangling bond at terminal end of RNA rosetta model

2012-12-26 Thread Gert Peters
Hi everybody, Im trying to use GROMACS for MD of a RNA model generated by Rosetta (FARFAR). As a test I try processing a modelledpdb file. When I prepare thetopology files (pdb2gmx -f test.pdb -ff amber99 -ignh ) from pdb I encounter following output : Sorting it all out... Opening force fiel