Re: [gmx-users] pyroglutamate in gromos53a6

Thank you Tsjerk, I am now trying with amber99.ff but have encountered the following problem: My PCA is at the N-terminus. I have an entry for [ NPCA ] in aminoacids.rtp and have updated aminoacids.r2b to include NPCA and I've even added an entry in aminoacids.hdb for NPCA. Yet when I

Re: [gmx-users] pyroglutamate in gromos53a6

Hi Henry, Apparently NPCA is not listed as being protein, so pdb2gmx assumes that the chain begins with GLY. Add NPCA to the file residuetypes.dat one directory up, with the designation 'Protein'. I think that should solve it. Groetjes, Tsjerk On Thu, Nov 24, 2011 at 6:59 PM, Henry Hocking

Re: [gmx-users] pyroglutamate in gromos53a6

Thank you Tsjerk, Now it works ! Cheers, Henry On 24 Nov 2011, at 23:11, Tsjerk Wassenaar wrote: Hi Henry, Apparently NPCA is not listed as being protein, so pdb2gmx assumes that the chain begins with GLY. Add NPCA to the file residuetypes.dat one directory up, with the designation

[gmx-users] pyroglutamate in gromos53a6

Dear all, Where can I find gromos53a6.ff parameters for pyroglutamate (PCA/ PGLU/ PGA) ? Alternatively, given that I have them in amber99.ff and oplsaa.ff is there a way I could adapt these to gromos53a6.ff? Can I use, for example, the gromos53a6.ff atom types from glutamine,

Re: [gmx-users] pyroglutamate in gromos53a6

Hi Henry, That would be a bit of a wild west approach. A better approximation would be taking the charges from the backbone amide group, as it is just an amide with on either side aliphatic carbons. Doing it properly is a bit more involved, as for the G53a6 FF you need to choose parameters giving