Re: [gmx-users] Re: Re: Pyroglutamic Acid - Topology (pdb2gmx)

2009-10-15 Thread Justin A. Lemkul
Tsjerk Wassenaar wrote: Hey, The problem comes from the special linkage between PGL and whatever the subsequent amino acid is - the amide is formed through the side chain. As such, you will need to specify a special bond in specbond.dat before this connectivity will be recognized. If this i

Re: [gmx-users] Re: Re: Pyroglutamic Acid - Topology (pdb2gmx)

2009-10-15 Thread Tsjerk Wassenaar
Hey, > The problem comes from the special linkage between PGL and whatever the > subsequent amino acid is - the amide is formed through the side chain.  As > such, you will need to specify a special bond in specbond.dat before this > connectivity will be recognized.  If this is successful, then th

Re: [gmx-users] Re: Re: Pyroglutamic Acid - Topology (pdb2gmx)

2009-10-15 Thread Justin A. Lemkul
Christian wrote: Justin Wrote: Did you add PGL to aminoacids.dat? Yes i added PGL to this file. How did you specify your termini? i'm not shure where i can define this - i only found such definitions in *rtp- file? Defining termini is done with pdb2gmx -ter, but as I think about it now

[gmx-users] Re: Re: Pyroglutamic Acid - Topology (pdb2gmx)

2009-10-15 Thread Christian
Justin Wrote: > Did you add PGL to aminoacids.dat? Yes i added PGL to this file. > How did you specify your termini? i'm not shure where i can define this - i only found such definitions in *rtp- file? the definitions there looks like this: [ PGL ] [ atoms ] Nopls_238 -0.500 1