[gmx-users] Coupling Molecule type in *mdp file for Free Energy Simulation
Hello, I want to calculate the pKa shift of a buried aspartic acid residue in my protein using alchemical free energy perturbation. I do not know how to represent the individual aspartic acid attached to the protein in the required couple-moltype entry of the *mdp file. Any suggestions would be much appreciated. Cheers, Jackson Chief Elk Graduate Student The University of Montana Biophysics and Biochemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] grompp is adding a bond in my model that should not be there
I made a model of a receptor protein, bilayer, and solvent. My protein contains a 20 residue gap. This gap corresponds to a region of the protein that had been digested by trypsin before crystallization. The trypsin digestion has no affect on receptor activity experimentally. I performed energy minimization without problem. The protein looked like it should, containing the gap. When I performed equilibration, the output had the C-terminus of one protein fragment connected to the N-terminus of the other protein fragment. I don't know how this peptide bond was created, because it was not in the input *.gro file to grompp. Please help. Jackson Chief Elk Graduate Student in Biophysics and Biochemistry The University of Montana Missoula, MT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] grompp is adding a bond in my model that should not be there
The missing residues correspond to a loop that connects two alpha helices. The C-terminal end of one helix, and N-terminal end of the other helix contain a random coil. After energy minimization, the coils are extended in space and not connected. I visualized this by looking at the .gro file in VMD. After 5ns of unrestrained MD, the two coils are clearly connected by looking at the output .gro file in VMD. Weird. On Sun, Mar 25, 2012 at 9:48 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 26/03/2012 12:20 PM, Jackson Chief wrote: I made a model of a receptor protein, bilayer, and solvent. My protein contains a 20 residue gap. This gap corresponds to a region of the protein that had been digested by trypsin before crystallization. The trypsin digestion has no affect on receptor activity experimentally. I performed energy minimization without problem. The protein looked like it should, containing the gap. You have to treat this gap somehow. Either you have to cap the peptide chains (see pdb2gmx -h), or model in the missing residues using some (non-GROMACS) software. When I performed equilibration, the output had the C-terminus of one protein fragment connected to the N-terminus of the other protein fragment. I don't know how this peptide bond was created, because it was not in the input *.gro file to grompp. Please help. .gro files have coordinates, never bonds. Since you haven't described how you are treating the gap, and haven't said how you've observed the creation of a peptide bond, it's hard to give specific guidance. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error when performing grompp on lipid bilayer modeled with CHARMM27
I want to make a model of a GPCR inserted into lipid bilayer. I obtained the structure file for a solvated POPC bilayer from the CHARMM-GUI site. I used CHARMM27 force field to model the bilayer and *pdb2gmx *had no problem generating the *.gro, *.top, and posre.itp files. When I perform *grompp* I receive the following warning and error; WARNING 1 [file ffnonbonded.itp, line 130]: Overriding atomtype HOL ERROR 1 [file bilayer.top, line 271489]: No default U-B types I though that the issue with creating Urey-Bradley interactions using *pdb2gmx *had been corrected in Gromacs-4.5.4. Please give me some advice on how to proceed further. Thank you, Jackson Chief Elk -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
