[gmx-users] Re: Atom O5 not found in residue seq.nr. 1 while adding atom

I forgot to mention that i am using OPLS-AA/L all-atom force field. On Fri, Mar 9, 2012 at 11:21 AM, pragna lakshmi pragna...@gmail.com wrote: Dear Gromacs Users, I need to simulate a protein that has N-acetyl glucosamine (NAG). Since NAG residue is not present in residue

Re: [gmx-users] Re: Atom O5 not found in residue seq.nr. 1 while adding atom

On 9/03/2012 4:56 PM, pragna lakshmi wrote: I forgot to mention that i am using OPLS-AA/L all-atom force field. On Fri, Mar 9, 2012 at 11:21 AM, pragna lakshmi pragna...@gmail.com mailto:pragna...@gmail.com wrote: Dear Gromacs Users, I need to simulate a protein that

Re: [gmx-users] Re: Atom O5 not found in residue seq.nr. 1 while adding atom

Thank u so much Mark. Is there any parameterization to mention forcefield and co ordinates in aminoacids.rtp in the fields of atoms, bonds (like C1opls_195 +0.3651 ). I checked the co ordinates in .pdb and .rtp files. Both are not the same. On Fri, Mar 9, 2012 at 11:56 AM, Mark