Re: [gmx-users] LINCS WARNING after good minimization and equilibration (NPT and NVT)

Thank you! I will try to change something and write to you about the result . -- Sincerely, Yulian Gavrilov -- 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

[gmx-users] IMPLICIT SOLVENT IN AMBER

/mol/Angstrom^2. sa_surface_tension = 2.092 -- Sincerely, Yulian Gavrilov -- 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

Re: [gmx-users] IMPLICIT SOLVENT IN AMBER

OBC} > and the non-polar solvation is calculated using > sa_algorithm=Ace-approximation. > > Cheers > /Per > > 10 mar 2011 kl. 10.10 skrev Yulian Gavrilov: > > Dear, all > I just begin to work in gromacs. > I would like to run on a protein with amber99. > Is there

Re: [gmx-users] IMPLICIT SOLVENT IN AMBER

in an implicit solvent. > Do deal with that properly one should use an implicit salt concentration, > but that is not implemented currently. > The choice of water-model with pdb2gmx is not important. You can choose > 'None' here. > > Cheers > /Per > > 10 mar

[gmx-users] isopeptide bond

t this bond is not good. Please can you advice me how yo make this isopeptide bond good? Can I just remove this hydrogens? -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] isopeptide bond

, pymol). When I look on step...pdb, one these residues is exploded (it's atoms are far from each other outside of the water box). 2011/3/13 Mark Abraham > On 13/03/2011 8:55 PM, Yulian Gavrilov wrote: > > Dear gmx users, > > I just started with gromacs. > > Can you

Re: [gmx-users] isopeptide bond

Yes, I checked topol.top. There are all isopeptide bonds ,that I want (according to atom contacts, angles, etc.) 2011/3/13 Mark Abraham > On 13/03/2011 9:53 PM, Yulian Gavrilov wrote: > > Thank you! > > I use the correct “O” in Gly according to .rtp and I checked it with

Re: [gmx-users] isopeptide bond

440 2441 1 2440 2442 1 2442 2443 1 2442 2444 1 2442 2445 1 2445 2446 1 -- Sincerely, Yulian Gavrilov -- 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 befo

[gmx-users] ffamber99.hdb

3HZNZCECD ** Sincerely, Yulian Gavrilov -- 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)subs

Re: [gmx-users] isopeptide bond

Abraham > > > On 14/03/11, *Yulian Gavrilov * wrote: > > Dear, Mark > > You asking about this (?): > > According to ffamber99.atp: > > amber99_34 14.01000 ; N sp2 nitrogen in amide groups > > amber99_39 14.01000 ; N3 sp3 N for charged amino groups (Lys, e

Re: [gmx-users] isopeptide bond

Thanks! I understand it, but I had several errors about it. Without adding of (HP CT N) [angletype] it does not work. How to force it to take its type from its current environment, not its historical one? 2011/3/15 Mark Abraham > > > On 15/03/11, *Yulian Gavrilov * wrote: >

[gmx-users] g_mdmat distance matrices

get a matrices with numbers? -- Sincerely, Yulian Gavrilov -- 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)subs

[gmx-users] average trajectory

to use *xpm2ps* to get average matrix, but in it I can only combine matrices (not to take an average matrix). Can I get an average matrix, or an average trajectory? -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

[gmx-users] trjconv and g_filter

these residues are within loops. It seems normal, that they move more than others. But 4.5 angstroms – is it ok? As I understand *g_filter* is used more to make good movies, but without it I get strange RMSF. Can I use g_filter instead of using trajconv or after trajconv? -- Sincerely, Yulian Gav

[gmx-users] make a new bond in VERSION 4.5.4

LYQ GLQ (it works ok) -- Sincerely, Yulian Gavrilov -- 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 req

Re: [gmx-users] make a new bond in VERSION 4.5.4

umentation/File_Formats/Topology_File But as you see from the previous mail, I included LYQ and GLQ to the force field. Maybe I missed something? -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv

Re: [gmx-users] make a new bond in VERSION 4.5.4

CA +N C O [ GLQ ] [ atoms ] N N -0.41570 1 H H 0.27190 2 CA CT -0.02520 3 HA1 H1 0.06980 4 HA2 H1 0.06980 5 C C 0.59730 6 O O -0.56790 7 [ bonds ] N H N CA CA HA1 CA HA2 CA C C O -C N [ impropers ] -C CA N H CA +N C O -- Sincerely, Yulian Gavrilov -- gmx-users mailing

Re: [gmx-users] make a new bond in VERSION 4.5.4

-- Sincerely, Yulian Gavrilov -- 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