Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

Great! I had already setup my git copy. No need for it. Strange atom names as usual. So we can already start our metalloenzyme simulation. Great software and support. Thank you Mark and Justin! 2016-04-22 21:49 GMT-03:00 Justin Lemkul : > > > On 4/22/16 8:40 PM, Pedro Lacerda

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

On 4/22/16 8:40 PM, Pedro Lacerda wrote: Applying the same simple conversion to the vdw parameters for atoms Mg+2 (id 46), Ca+2 (id 47), and Zn+2 (id 48) found in amber99.prm of the TINKER package, which is the base of Sorin parameters, there is agreement between Mg+2 and Zn+2. It looks like

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

Applying the same simple conversion to the vdw parameters for atoms Mg+2 (id 46), Ca+2 (id 47), and Zn+2 (id 48) found in amber99.prm of the TINKER package, which is the base of Sorin parameters, there is agreement between Mg+2 and Zn+2. It looks like a bug in the L-J parameters of TINKER package

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

For me they must be the same in both force fields amber99sb-ildn, amber99, at the paper, etc. If it is different then should be another force field, isn't it? About the conversion, I did it wrong on my spreadsheet. Sorry... It works! Many thanks! Except for the epsilon of Ca+2. I verified the

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

On 4/22/16 6:24 PM, Pedro Lacerda wrote: Thank you! According to [1, Table 2a], these are the L-J (6-12) parameters for Ca2+ used at AMBER package. Or the paper or GROMACS copied wrongly from the AMBER package source because simple unit conversion gives different results. That paper was

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

Thank you! According to [1, Table 2a], these are the L-J (6-12) parameters for Ca2+ used at AMBER package. Or the paper or GROMACS copied wrongly from the AMBER package source because simple unit conversion gives different results. I don't own a copy of AMBER package, please could you verify the

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

On 4/21/16 4:30 PM, Pedro Lacerda wrote: Hi Mark, I starting converting from AMBER (according to the paper) to GROMACS and comparing the results. Please explain in more words what this constant of two mean or how can I handle it. Ignoring it and just converting the units, I got these results

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

Hi Mark, I starting converting from AMBER (according to the paper) to GROMACS and comparing the results. Please explain in more words what this constant of two mean or how can I handle it. Ignoring it and just converting the units, I got these results AMBER (table 2a) Rmin/2 (Å) epsilon

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

Very thanks, I'm trying it right now. Pedro Lacerda 2016-04-18 21:29 GMT-03:00 Mark Abraham : > Hi, > > Convert the units and absorb the factor of two to the minus six. Compare > with other ions present in both representations of such force fields. > > Mark > > On

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

Hi, Convert the units and absorb the factor of two to the minus six. Compare with other ions present in both representations of such force fields. Mark On Tue, 19 Apr 2016 02:21 Pedro Lacerda wrote: > Hi Gromacs users, > > We are planning a simulation with a metallic