Re: [gmx-users] mismatch sol.gro/topol.gro

much users and maintainers for the much aid I received. In spite of unsuccessful work, i am happy to have had the opportunity to see how the preparation for gromacs is carried out. cheers francesco pietra On Wed, Nov 28, 2018 at 6:42 PM Francesco Pietra wrote: > I am preparing (as a newcomer

[gmx-users] mismatch sol.gro/topol.gro

I am preparing (as a newcomer to gromacs) a complex of a protein with two ligands. One is the universal GDP, the other one a diterpenoid. GROMCS2018, CGenFF, CHARMM36. The output of addions complains about GDP.prm (the GDP.str of CGenFF origin had no problems for NAMD/CHARMM36) and (because of thi

Re: [gmx-users] scp216.gro

ck > the gromacs directory to see if the file is absent. > > > Kind regards > > > Kenneth > > > > Van: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> namens France

[gmx-users] scp216.gro

I am attempting solvation of a protein-ligand complex following the lines of the same name tutorial. Lacking scp216.grow. Where to find it and why it is not included in gromacs 2018 (as provided by Debian amd64 buster)? thanks for advice francesco pietra -- Gromacs Users mailing list * Please

[gmx-users] Fwd: Mismatch between gromacs and python-networkx versions

, as the ligand_ini.pdb looks like to be correct fp -- Forwarded message - From: Francesco Pietra Date: Mon, Nov 26, 2018 at 6:25 PM Subject: Re: [gmx-users] Mismatch between gromacs and python-networkx versions To: This is to let you know, that the fixed .mol2 (got by first

Re: [gmx-users] Mismatch between gromacs and python-networkx versions

thanks again On Mon, Nov 26, 2018 at 3:57 PM Justin Lemkul wrote: > > > On 11/25/18 9:10 AM, Francesco Pietra wrote: > > This is my first post to gromacs, to which I came in the hope that FEP > > simulations are more efficient than with other engines. > > > > I upd

[gmx-users] sort_mol2_bonds.pl issues

11 C4' 326.9510 449.9750 310.0480 C.3 501 GDP 0.1133 12 O4' 326.8250 448.7650 310.8190 O.3 501 GDP-0.3456 13 C3' 328.4210 450.0360 309.6490 C.3 501 GDP 0.1135 Did not find anything about on Internet. Thanks fo

[gmx-users] sort_mol2_bonds.pl issue

C.3 501 GDP 0.1133 12 O4' 326.8250 448.7650 310.8190 O.3 501 GDP-0.3456 13 C3' 328.4210 450.0360 309.6490 C.3 501 GDP 0.1135 Did not find anything about on Internet. Thanks for advice francesco pietra -- Gromacs Users mailing

[gmx-users] Mismatch between gromacs and python-networkx versions

This is my first post to gromacs, to which I came in the hope that FEP simulations are more efficient than with other engines. I updated debian amd64 from stretch to buster in order to have the said preferred gromacs 2018 (2016 on stretch). Now, to set up the system (protein+ligands) I have networ

[gmx-users] FEP from .top gathered with TOPOGROMACS from NAMD-CHARMM MD

to add flags and restraints after the MD equilibration. With NAMD, FEP flags and restraints are simply added to the general MD configuration file. Thanks for advice. francesco pietra -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX