Re: [gmx-users] Missing Residues are list ind pdb file

Hi, Note, that this is indeed the size of the charge groups in the CHARMM force field. You could run pdb2gmx -nochargegrp if you know what you're doing. Regards, Pär Bjelkmar > I think the notes from grompp are pretty clear. You need to redivide > your charge groups so that they contain fewe

Re: [gmx-users] Missing Residues are list ind pdb file

Hi Jack, On Fri, Jan 15, 2010 at 8:05 PM, Jack Shultz wrote: > I'm trying to prep Fe-Hydrogenase again (1YQW). I took out all the > non-standard residues. Re-named n-terminal and c-terminal residues. Took out > connects because that worked last time though I'm uncertain if connect > really mater

[gmx-users] Missing Residues are list ind pdb file

I'm trying to prep Fe-Hydrogenase again (1YQW). I took out all the non-standard residues. Re-named n-terminal and c-terminal residues. Took out connects because that worked last time though I'm uncertain if connect really maters. Another issue with preping a protein. Its says I a missing H and HA

Re: [gmx-users] Missing Residues

sunny mishra wrote: Hi All, My protein has lots of missing residues and in every chain there are 4-5 missing residues with atom name. I can see missing residues with the help of Swiss PDB Viewer after I load the pdb file. I am very new in Swiss PDB viewer and I would highly appreciate if an

[gmx-users] Missing Residues

Hi All, My protein has lots of missing residues and in every chain there are 4-5 missing residues with atom name. I can see missing residues with the help of Swiss PDB Viewer after I load the pdb file. I am very new in Swiss PDB viewer and I would highly appreciate if anyone can let me know how to

Re: [gmx-users] missing residues

One possibility is Modloop: http://alto.compbio.ucsf.edu/modloop/modloop.html ...which is a function of MODELLER: http://salilab.org/modeller/ --Tom On Apr 6, 2006, at 2:25 PM, Jayant James Jayasundar wrote: Hi friends! Part of a molecule that I am trying to simulate is not crystallograph

Re: [gmx-users] missing residues

At 06:25 PM 4/6/2006 +, you wrote: Hi friends! Part of a molecule that I am trying to simulate is not crystallographically resolved. To be exact about 17 amino acids from 136-148. Please suggest suggestions on how? I go about building these missing residues and integrating with the crysta

Re: [gmx-users] missing residues

Quoting Jayant James Jayasundar <[EMAIL PROTECTED]>: Hi friends! Part of a molecule that I am trying to simulate is not crystallographically resolved. To be exact about 17 amino acids from 136-148. Hi Are those residues in the Nter/Cter ? If they are, perhaps leaving the protein without

[gmx-users] missing residues

Hi friends! Part of a molecule that I am trying to simulate is not crystallographically resolved. To be exact about 17 amino acids from 136-148. Please suggest suggestions on how? I go about building these missing residues and integrating with the crystallographically resolved structure such that