[gmx-users] quantum chemistry to gromacs topology approaches

Hi, What approaches do you know of for going from quantum chemistry software to gromacs topology for new protein residues? The one I am presently using is an AmberTools antechamber/gaussian/leap toolchain to define new residues, then amb2gmx.pl to convert to gromacs topology. Do you know of any ot

Re: [gmx-users] Imposing distance restraints between two

Hi, those aren't angstroms, theyre nm 1.128 1.138 On Fri, Aug 15, 2008 at 9:16 AM, <[EMAIL PROTECTED]> wrote: > Dear colleagues, > I thank Justin for your suggesting me the distance > restraints.So, if I want to impose a distance restraint for 11.28 A between > two atoms

[gmx-users] AMOEBA in gromacs

Hi all, Is it the case that the gromacs simulation engine can not presently make use of the AMOEBA force field? i.e. it is not possible to use amb2gmx on amoeba topology and coordinates output from amber's leap and have the result executed by gromacs? I see a flag is set in amber simulation engine

[gmx-users] forcefields gaff/ff02EP good solvated with SPCBOX but not POL3BOX

Does anyone know why POL3 with gaff and ff02EP in amber antechamber/tleap would lead to unstable simulations but when POL3 is replaced with SPC (solvating with POL3BOX replaced by solvating by SPCBOX) the simulation becomes stable? I use amb2gmx to run the simulation on gromacs. ___

[gmx-users] generating topology for artificial residues

Hi all,   What approach to use to generate a topology file for peptides which include artificial residues such as serine with its sidechain extended by two carbons to double bond with another such residue i.e. CA-CB-OG-C1-C3=C4-C2-OG-CB-CA   Also I need to generate a topology for another type of

[gmx-users] specbond # bonds

Hi, does the following specbond.dat line build a double bond between the two atoms?  CHU    C3      2      CHV    C4      2      0.2    CHU    CHV What would happen if the first number was 2 but the second number was 1 ? Would two C4s need to be at the right distance away from the one C3? Thanks,  

Re: [gmx-users] specbond recognised but not built

Thankyou very much Tsjerk, indeed this was the problem. I am most relieved this was the solution. I had assumed the distance was an upper bound on the acceptable distance. - Original Message From: Tsjerk Wassenaar <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Sunday,

[gmx-users] specbond recognised but not built

Hi all,   I am using gromacs 3.3.3, and have a specbond definition: CHU C3  2   CHV C4  2   0.2 CHU CHV This is recognised but not built: 7 out of 7 lines of specbond.dat converted successfully Special Atom Distance matrix:     CHU5