[gmx-users] gromos parameterisation in OPLS
Justin A. Lemkul
jalemkul at vt.edu
Tue Jun 17 12:30:26 CEST 2008
If you include in the .itp file all the necessary combinations in those
sections, then yes, the .itp file is reasonable and will use the OPLS-AA
parameters for those specified items. Take care to get the numbering
right after that point, because you will likely be inserting lots of
ANINDITA GAYEN wrote:
> If i insert the hydrogen atoms in the first section of the itp file, where atomnames , atomtypes , nr, cgnr are displayed, wil it be wrong. Also, i was talking that, will the inclusion of "ffoplsaa.itp" will serve the bonded and nonbonded parameters if i supply the connectivities in all the bonds, pairs, angles and dihedral section by the atom numbers?
> Thanks for the requested answers.
> --- On Mon, 16/6/08, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> From: Justin A. Lemkul <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] gromos parameterisation in OPLS
>> To: aninditagayen at yahoo.co.in, "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> Date: Monday, 16 June, 2008, 9:29 PM
>> Changing the atomtypes will only work if you have explicit
>> inclusion of
>> all hydrogens in your PRODRG-generated topology. Since the
>> server outputs a GROMOS-based .itp file, this is unlikely
>> unless your
>> molecule contains only polar or aromatic groups. If
>> we're still talking
>> about CHAPS or cholesterol, this will not be the case. You
>> will have
>> nonpolar groups that, within GROMOS, are atomtype CH1, CH2,
>> etc., but
>> OPLS will not have these UA representations.
>> I'm not sure what you mean in the last sentence.
>> Nothing in this
>> process will be automatically generated for you.
>> You're building your
>> topology by hand. Inclusion of "ffoplsaa.itp"
>> will tell grompp which
>> parameters (bonded and nonbonded) apply to your molecule.
>> "ffoplsaa.itp" will not tell any Gromacs program
>> to automatically detect
>> and generate bonds, dihedrals, etc.
>> The only way to have "automatic" generation of
>> these parameters is to
>> build an .rtp entry for your molecule that contains all of
>> information as well, and process your structure with
>> pdb2gmx. This is
>> just as much work as building the topology yourself, I
>> ANINDITA GAYEN wrote:
>>> I came to know from the mailing list that if i only
>> change the atomtype in the output itp file of PRODRG2 and
>> put the charges as optimised by Gaussian; provided i
>> include #include ffoplsaa.itp in the .top file of the new
>> molecule and just keep the atom mumbers in [bonds],
>> [pairs], [angles] and [dihedrals] as found in the the all
>> atom pdb of PRODRG2, the resultant top file will be a top
>> file in OPLS format. It was also stated there in the
>> mailing list that for the atom numbers mentioned the opls
>> staff will put the parameter values necccesary for the
>> [bonds], [angles] etc.
>>> Is the approach right?
>>> From Chandigarh to Chennai - find friends all
>> over India. Go to
>>> gmx-users mailing list gmx-users at gromacs.org
>>> Please search the archive at
>> http://www.gromacs.org/search before posting!
>>> Please don't post (un)subscribe requests to the
>> list. Use the
>>> www interface or send it to
>> gmx-users-request at gromacs.org.
>>> Can't post? Read
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
> Connect with friends all over the world. Get Yahoo! India Messenger at http://in.messenger.yahoo.com/?wm=n/
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users