[gmx-users] Improper dihedral parameters for peptide bond
Dear All, I would like to make sure whether these parameters O X X C 2 0. 1004.16 NH1 X X H 2 0. 167.36 under [ dihedraltypes ] card in ffbonded.itp file are the improper dihedral parameters for the peptide bonds as defined in aminoacids.rtp file with the following statement: [ impropers ] N -C CA HN C CA +N O If so, why isn't it C X X O if the first atom should be the to which all the others are connected? Best Regards, Dawid PS I have sent the same question to a different address. I apologize if I doubled the topic. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Amide hydrogen naming in charmm 36 forcefield
On 7/20/19 1:05 AM, Dilip.H.N wrote: Sir, I have also tried with atom name H, (i have checked in the .rtp file and is named as 'H'), but still i am getting the same following error: Atom HN in residue NMA 1 was not found in rtp entry NMA with 12 atoms while sorting atoms. First, i tried with naming the amide hydrogens as 'H' and got the above-mentioned error and then i followed the link https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-May/088942.html which stated "CHARMM has unique nomenclature for amide H atoms, so H needs to be renamed HN, though unfortunately, that's also wrong in the .rtp file. I'll fix that for the future." and hence i changed the 'H' into 'HN'. In spite in both the cases (naming the amide hydrogens as 'H' or 'HN'), i am getting the errors. Probably the force field .arn file is responsible for this problem, by renaming all H to HN, which is actually incorrect for NMA. The amide nitrogens are not defined in the .hdb files in charmm36 FF too. We have to write the .hdb entries by hand so we only create the ones we find useful. If you want to write one and verify it works, I can include it in a future version. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Drude force field
On 7/20/19 12:26 AM, Myunggi Yi wrote: Dear Justin, I've followed the instructions, and I prepared my system. I've got the following error message. " No default Bond types." There are several errors. The bond is between atoms 43 and 45, and the following is a part of the dmpc.itp, which is generated by pdb2gmx with drude-2013f_2018_10.ff 43 OD30CL 1 DMPCO21 43 1.484715.5994 ; qtot 1.803 44 DRUD 1 DMPC DO21 44-1.4847 0 ; qtot 0.318 45LPD 1 DMPC LPMA 45 -0.17 0 ; qtot 0.148 46LPD 1 DMPC LPMB 46 -0.17 0 ; qtot -0.022 47 CD2O3B 1 DMPCC21 472.72816 11.611 ; qtot 2.706 48 DRUD 1 DMPC DC21 48 -2.03116 0 ; qtot 0.675 It seems gromacs added a bond to them, which is not available in the dmpc.itp file. Is it common the bond between polar heavy atom and the lone pair virtual sites? There should be no bonds to lone pairs. It seems there is an error in the .rtp entry for the lipid. The conversion script I used explicitly removes these but clearly there is some kind of bug that's not catching this. I will look into it. For now, simply remove any LP references in [bonds] and regenerate the topology. Program information: GROMACS: gmx grompp, version 2016-dev-20181220-a2cab74 Command line: gmx grompp -f em.mdp -c ../gg.gro -r ../gg.gro -p ../topol.top -o em.tpr In addition, I do have not integer total charge. NOTE 2 [file topol.top, line 49]: System has non-zero total charge: -0.000464 Of course, when I generate the protein itp, the total charge was 0.00. As you know DMPC is neutral too. After combine protein, dmpc, water, this happened. That's just rounding error. You're going to encounter this a lot due to the large number of fractionally charged particles in a polarizable system. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Improper dihedral parameters for peptide bond
Dear All, I would like to make sure whether these parameters O X X C 2 0. 1004.16 NH1 X X H 2 0. 167.36 under [ dihedraltypes ] card in ffbonded.itp file are the improper dihedral parameters for the peptide bonds as defined in aminoacids.rtp file with the following statement: [ impropers ] N -C CA HN C CA +N O If so, why isn't it C X X O if the first atom should be the to which all the others are connected? Best Regards, Dawid -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] inexplicable rmsf error - Too many iterations in routine JACOBI
Hi, ..just as a follow up with more information: When I use gmx trajconv to extract snapshots that contain only the molecule of interest from my original "full" .xtc file, for my RMSF calculation, (using the same index as before) and then use gmx rmsf -f traj.pdb instead of on the traj.xtc, it works fine. So there is some reason that using the .xtc file leads to this error, and only when my reference structure contains only the molecule of interest. Is there an explanation for why I'm seeing this bug? Is my .xtc file somehow corrupted in a weird way? Or is it likely fine but gmx rmsf is finicky and so using the .pdb trajectory, so long as it works, is fine, and this bug shouldn't indicate an issue with my .xtc file? Thanks for any info... Mala On Fri, Jul 19, 2019 at 5:28 AM Mala L Radhakrishnan wrote: > Hi all, > > I am trying to run gmx RMSF using.a particular snapshot as my reference > structure (-s option). > > When I extract a gro file to make my reference structure that has only the > molecule that INCLUDES the alpha-carbons in my index file that I want to > use for my RMSF calculation (I checked), then midway through its reading in > the frames (and not always at the same point) I get the following error: > > Program: gmx rmsf, version 2016.3 > Source file: src/gromacs/linearalgebra/nrjac.cpp (line 165) > > Fatal error: > Error: Too many iterations in routine JACOBI > > When I extract a gro file that has an even larger subset of the atoms in > the frame than the one requested previously, it seg-faults right away. > > But when I extract a snapshot that has the *entire* system to use as my > reference structure (all atoms, including solvent and ions), it seems to > work. I am using the same .xtc file and index file in all cases, just > changing the -s file. > > Googling the error suggests that I have a mismatch somewhere in my index > file and/or structure file, but (a) I have checked this by eye and can't > find any mismatches and (b) when I do he same sort of extraction of a > subset of the system on several other trajectories it works just fine -- in > other words, this seems to be the only trajectory where I need to extract > the entire system (including solvent, ions, etc.) as my reference frame > just to get an rmsf of alpha carbons in the protein molecule of interest. I > am using version 2016.3. I have tried multiple gromacs versions to extract > and run just in case but got the same error. The reference structure also > appears to be structurally fine (no broken molecules, etc.) > > What could be different about this trajectory that is causing the problem? > Again, I looked by eye at the gro file I'm using as my reference structure > and made sure that it contains all the atoms in the index file selection > I'm using for my RMSF calculation... > > Thanks for any help. I am happy to send you the files for which it works > and for which it doesn't...just very confused! > > Mala > > > > -- > Mala L. Radhakrishnan > Associate Professor of Chemistry > Director, Biochemistry Program > Wellesley College > 106 Central Street > Wellesley, MA 02481 > (781)283-2981 > -- Mala L. Radhakrishnan Associate Professor of Chemistry Director, Biochemistry Program Wellesley College 106 Central Street Wellesley, MA 02481 (781)283-2981 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
