Re: [gmx-users] unknown cmap torsion between atoms

2012-05-25 Thread Justin A. Lemkul
On 5/25/12 5:04 PM, Steven Neumann wrote: On Fri, May 25, 2012 at 2:34 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: On 5/25/12 5:52 AM, Steven Neumann wrote: Dear Gmx Users, My system is made of 3 proteins. As I want to use distance restraints dynamics

Re: [gmx-users] unknown cmap torsion between atoms

2012-05-25 Thread Steven Neumann
On Fri, May 25, 2012 at 2:34 PM, Justin A. Lemkul wrote: > > > On 5/25/12 5:52 AM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> My system is made of 3 proteins. As I want to use distance restraints >> dynamics >> between atoms belonging to each of them I have to produce topoloy with one >> mo

Re: [gmx-users] unknown cmap torsion between atoms

2012-05-25 Thread Justin A. Lemkul
On 5/25/12 5:52 AM, Steven Neumann wrote: Dear Gmx Users, My system is made of 3 proteins. As I want to use distance restraints dynamics between atoms belonging to each of them I have to produce topoloy with one moleculetype. I used pdb2gmx -chainsep interactive (I used merge: yes). Then when

Re: [gmx-users] unknown cmap torsion between atoms

2012-05-25 Thread Steven Neumann
On Fri, May 25, 2012 at 4:18 PM, Mark Abraham wrote: > On 25/05/2012 7:52 PM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> My system is made of 3 proteins. As I want to use distance restraints >> dynamics between atoms belonging to each of them I have to produce topoloy >> with one moleculetyp

Re: [gmx-users] unknown cmap torsion between atoms

2012-05-25 Thread Mark Abraham
On 25/05/2012 7:52 PM, Steven Neumann wrote: Dear Gmx Users, My system is made of 3 proteins. As I want to use distance restraints dynamics between atoms belonging to each of them I have to produce topoloy with one moleculetype. I used pdb2gmx -chainsep interactive (I used merge: yes). Then

Re: [gmx-users] unknown cmap torsion between atoms

2011-10-31 Thread Mark Abraham
On 1/11/2011 2:16 PM, ram bio wrote: Hi Mark, Thanks for the response. I have built this system (protein in popc bilayer using charmm GUI) and submitted the total built system to pdb2gmx, is this the reason for having unknown CMAP torsion while executing grompp, by the way pdb2gmx doesnot sho

Re: [gmx-users] unknown cmap torsion between atoms

2011-10-31 Thread ram bio
Hi Mark, Thanks for the response. I have built this system (protein in popc bilayer using charmm GUI) and submitted the total built system to pdb2gmx, is this the reason for having unknown CMAP torsion while executing grompp, by the way pdb2gmx doesnot show any error. Cant the charmm gui built sys

Re: [gmx-users] unknown cmap torsion between atoms

2011-10-31 Thread Mark Abraham
On 1/11/2011 1:24 PM, ram bio wrote: Dear Gromacs users, I have built a protein embedded in popc bilayer and executed pdb2gmx using charmm27 ff on the system and the toplogy file was created without errors, but when wanted to minimise the system with grompp i am getting an error as : unknown