Re: [gmx-users] charmm36 force field

2018-02-14 Thread Justin Lemkul
On 2/12/18 3:09 PM, farial tavakoli wrote: First, please note that this line is not doing anything: define        =  -DUSE_OLD_C3 If you're trying to use the old CHARMM36 parameters, and not CHARMM36m, the correct keyword is -DUSE_OLD_C36. We only included that in the case that people

Re: [gmx-users] CHARMM36 force field available for GROMACS

2014-04-10 Thread gsettanni
Hi Justin and Roland, we are interested in simulating a glycosilated protein. We already have a pdb file (and psf topology) with the charmm/namd format/nomenclature. We managed to have pdb2gmx read the carbohydrate residues by adding the relative entries in the residuetypes.dat, however we have

Re: [gmx-users] CHARMM36 force field available for GROMACS

2014-04-10 Thread Justin Lemkul
On 4/10/14, 2:51 AM, gsettanni wrote: Hi Justin and Roland, we are interested in simulating a glycosilated protein. We already have a pdb file (and psf topology) with the charmm/namd format/nomenclature. We managed to have pdb2gmx read the carbohydrate residues by adding the relative

Re: [gmx-users] CHARMM36 force field available for GROMACS

2014-03-18 Thread Justin Lemkul
Hi All, To follow up on a few recent issues that we have discovered and/or have been reported here, we have updated our CHARMM36 force field files. As always, they can be downloaded from: http://mackerell.umaryland.edu/CHARMM_ff_params.html Here is a list of changes: 1. An error in

Re: [gmx-users] CHARMM36 force field available for GROMACS

2014-03-18 Thread Gmail2
Dear Justin, Did you provide/add the parameters for Zn bound to OH- (hydroxide ion) and Zn bound to H2O (water) in updated CHARMM36 ff? For example, this state is important for some structures. E.g. Carbonic anhydrase. Ahmet Yıldırım 18 Mar 2014 tarihinde 18:44 saatinde, Justin Lemkul

Re: [gmx-users] CHARMM36 force field available for GROMACS

2014-03-18 Thread Justin Lemkul
On 3/18/14, 1:32 PM, Gmail2 wrote: Dear Justin, Did you provide/add the parameters for Zn bound to OH- (hydroxide ion) and Zn bound to H2O (water) in updated CHARMM36 ff? For example, this state is important for some structures. E.g. Carbonic anhydrase. No. We don't have any special

Re: [gmx-users] CHARMM36 force field available for GROMACS

2014-03-10 Thread Mark Abraham
Nice trick - I didn't realise you could chain and group sed regular expressions that way! Neither did I know pdb2gmx had an .arn database. That's two things I've learned... Can I go home now? :-D Mark On Mar 10, 2014 7:32 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: cat $pdbfile | sed

Re: [gmx-users] CHARMM36 force field available for GROMACS

2014-03-09 Thread Justin Lemkul
On 3/9/14, 6:28 AM, jim wrote: I'm confused about the existence of H5'1 and H5'2 atom names in the RNA nucleotides (in merge.rtp). I thought all atom names followed the CHARMM 36 atom name convention. Particularly, why do atoms H2' and H2'' correspond to the latter, while H5'1 and H5'2 carry

Re: [gmx-users] CHARMM36 force field available for GROMACS

2014-03-09 Thread Jim
Thanks for the clarification. *Bonds involving H5' and H5'' in RNA residues should indeed be changed to the H5'1 and H5'2 nomenclature.* Even though H5' and H5'' are connected to the same atom, what would be the problem to keep these H atom names H5' and H5'' instead of changing them to H5'1

Re: [gmx-users] CHARMM36 force field available for GROMACS

2014-03-09 Thread Jim
Thanks, but I'll have to ask you something again. :) On Sun, Mar 9, 2014 at 5:00 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/9/14, 7:23 PM, Jim wrote: Thanks for the clarification. *Bonds involving H5' and H5'' in RNA residues should indeed be changed to the H5'1 and H5'2