Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

whooops, never paid attention to the C N+, my bad, thank you Justin :) Ming On Mon, Jan 15, 2018 at 6:39 PM, Justin Lemkul wrote: > > > On 1/15/18 6:36 PM, MD wrote: > >> Sorry I didn't mean to connect it to the cmap. Yes it is a different >> question. How do I define a bond to

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

On 1/15/18 6:36 PM, MD wrote: Sorry I didn't mean to connect it to the cmap. Yes it is a different question. How do I define a bond to the +1 residue please? It is a side chain modified amino acid (LYS) and the backbone is unchanged. What else do I need to take care to make sure the backbone

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

Sorry I didn't mean to connect it to the cmap. Yes it is a different question. How do I define a bond to the +1 residue please? It is a side chain modified amino acid (LYS) and the backbone is unchanged. What else do I need to take care to make sure the backbone still connects? Thanks a bunch,

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

On 1/15/18 6:25 PM, MD wrote: I mean it is disconnected after energy minimization, i found out the CO is not connecting with the NH from the +1 amino acid. The structure was intact before the simulation. That has nothing to do with CMAP, that means you didn't properly define a bond to the

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

I mean it is disconnected after energy minimization, i found out the CO is not connecting with the NH from the +1 amino acid. The structure was intact before the simulation. Ming On Mon, Jan 15, 2018 at 6:23 PM, MD wrote: > Hi another quick question, what do you think could

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

Hi another quick question, what do you think could be the problem if the modified amino acid is not connecting to the +1 amino acid? the [cmap ] in merged.rtp already has the [ cmap ]-C NCA C+N Ming On Mon, Jan 15, 2018 at 3:09 PM, Justin Lemkul wrote: > >

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

Thank you so much for the guide Justin! The path looks clearer to me now :) Ming On Mon, Jan 15, 2018 at 3:09 PM, Justin Lemkul wrote: > > > On 1/15/18 2:56 PM, MD wrote: > >> updated, I figured it is because my N and CA have different type names >> than >> charmm, which is

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

On 1/15/18 3:06 PM, MD wrote: I wonder if there is a way I can create my own cmap for those modified type names and incorporate the cmap to the cmap.itp? That will end up being far more work than a proper parametrization of the side chain while leaving the backbone alone at standard atom

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

On 1/15/18 2:56 PM, MD wrote: updated, I figured it is because my N and CA have different type names than charmm, which is weird cause I used CHARMM GUI to get the itp files for the modified amino acid. Would it be an easy fix if I manually change those two atom names or I should go a

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

I wonder if there is a way I can create my own cmap for those modified type names and incorporate the cmap to the cmap.itp? Thanks, Ming On Mon, Jan 15, 2018 at 2:56 PM, MD wrote: > updated, I figured it is because my N and CA have different type names > than charmm, which is

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

updated, I figured it is because my N and CA have different type names than charmm, which is weird cause I used CHARMM GUI to get the itp files for the modified amino acid. Would it be an easy fix if I manually change those two atom names or I should go a different route for the cmap problem?