Thank you, sir. That's nice of Gromacs to automatically assign new atom types from an input pdb file. I check out the link as well.
--- On Mon, 2/21/11, Justin A. Lemkul <[email protected]> wrote: From: Justin A. Lemkul <[email protected]> Subject: Re: [gmx-users] on force fields To: "Discussion list for GROMACS users" <[email protected]> Date: Monday, February 21, 2011, 10:41 AM Mr Bernard Ramos wrote: > Thanks for the reply on my first querry. I have another one. If I add a NEW > atom type in *.atp file, will Gromacs automatically recognize this atom > type? Theoretically, yes, provided that you supply any corresponding parameters in, e.g., ffnonbonded.itp and ffbonded.itp. However, there is an unresolved bug related to atomtype assignment that may be relevant: http://redmine.gromacs.org/issues/618 It seems to me that any alterations to the .atp file cause things to break down, so do not be surprised if there are problems. -Justin > Thanks. > > > --- On *Wed, 2/16/11, Mark Abraham /<[email protected]>/* wrote: > > > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] on force fields > To: "Discussion list for GROMACS users" <[email protected]> > Date: Wednesday, February 16, 2011, 1:53 PM > > On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote: >> Hi everyone! >> I need to update the gromos force field 53A6 with the new force >> field 53ACARBO (JCC 10 NOV 2010). >> 1. I will have to change the parameter values in the file >> ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these >> the only files that I need to update if I need to switch to a new >> force field? >> > > You should make a copy of the whole force field directory into your > working directory, rename the new directory suitably, make a > suitable change to forcefield.doc, and then edit .itp files > suitably. This means you're leaving your reference version untouched > and can edit locally to your heart's content, and can be sure you're > selecting the right force field with pdb2gmx and/or in your .top file. > >> 2. The new force field 53ACARBO has a new gromos functional form >> for select torsional potentials. How to I go over implementing >> this in gromos? >> > > Preferably as a sum of existing functional forms. Or use tabulated > bonded interactions (see manual and wiki). > > Mark > > -----Inline Attachment Follows----- > > -- gmx-users mailing list [email protected] > <http://us.mc527.mail.yahoo.com/mc/[email protected]> > 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 > www interface or send it to [email protected] > ><http://us.mc527.mail.yahoo.com/mc/[email protected]>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] 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 www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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