But if the hydrogen has charge and its charge is not zero, then the total
charge of formyl wouldn't be zero! Make sense?
Sincerely,
Shima
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Sunday, May 13, 2012 9:44 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
pairs
On 5/13/12 1:06 PM, Shima Arasteh wrote:
> Even in gromos87, if I want to make a .rtp file for formyl, I need to put H
> atom
> in it? I mean, defining all atoms of a residue is necessary? Aren't the
> hydrogen
> atoms set by the gromacs package?
>
No. The presence of hydrogen atoms is set by the force field, not the software
that makes use of the force fields. In the Gromos force fields (and I
certainly
hope you're not using Gromos87, as it is ancient and better options are
available), polar H atoms are explicitly represented. In the case of an
aldehyde, I would strongly suspect you need an explicit H. I believe there
have
been recent publications regarding extensions of Gromos96 (note, NOT Gromos87)
that include such organic groups. Using those parameters may speed your
progress. If my recollection is incorrect and such parameters do not exist,
you
need to derive them yourself.
-Justin
> Cheers,
> Shima
>
> --------------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalem...@vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
> *Sent:* Sunday, May 13, 2012 8:36 PM
> *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in
> residue pairs
>
>
>
> On 5/13/12 11:43 AM, Shima Arasteh wrote:
> > Again thanks for all your replies.
> > As I got through your advices, I found that the atoms contribute in making
>bonds
> > and angles in a residue , or make dihedrals in a residue ( or with atoms
>in next
> > ones) plus the charge of a the residue should be defined properly in .rtp
>files
> > to define the new residue in aminoacid.rtp file of CHARMM36 force field.
> > So I arranged this lines to define formyl in .rtp file. And I got the
>topology.
> > But there are some questions for me here:
> >
> > 1. How can I be sure the formyl which I defined is correct? Is getting the
> > topology is enough to be sure of the correct output?
> >
>
> It is incorrect. As I said before, a formyl group is an aldehyde and has an H
> atom attached to C, e.g. -CH(=O). At present, you are defining a -C=O group
> with an incomplete carbon valence.
>
> http://en.wikipedia.org/wiki/Aldehyde
>
> > The .rtp file for formyl is as below:
> > [ For ]
> > [ atoms ]
> > ; name type charge chargegroup
> > C CTL1 0.5700 0
> > O O -0.5700 0
> > [angles ]
> > ai aj ak
> > O C +N
> > [ bonds ]
> > C O
> > C +N
> >
> > [ dihedrals ]
> > O C +N +CA
> >
>
> Aside from the missing atom (and resulting missing bonds, angles, and
> dihedral),
> the format of this entry is OK.
>
> > 2. There are lots of numbers in .itp file which I got through the
>swissparam.
> > But I think the charge of atoms may be useful in this file and also I can
>just
> > find the atoms contribute in bonds and angles and.... . Am I right? Or I
>may get
> > some other useful information which I can get through the files of
>swissparam?
> >
>
> If the existing bonded parameters for each interaction type (in ffbonded.itp)
> are sufficient for defining these interactions, then you can omit the content
> of
> the .itp file you've been using in the .rtp entry and rely on the force field
> to
> look up those values. There may be some interactions that are not in agreement
> (or do not exist), in which case you need to either define these parameters in
> the .rtp entry itself or in ffbonded.itp so that they will be detected by
> grompp
> later.
>
> -Justin
>
> > Thanks in advance, and sorry for disturbing you friends.
> > Shima
> >
> >
>--------------------------------------------------------------------------------
> > *From:* Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
> > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org
> <mailto:gmx-users@gromacs.org>>
> > *Sent:* Saturday, May 12, 2012 10:12 PM
> > *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in
> residue pairs
> >
> >
> >
> > On 5/12/12 1:37 PM, Justin A. Lemkul wrote:
> > >
> > >
> > > On 5/12/12 1:32 PM, Shima Arasteh wrote:
> > >> Dear gmx users,
> > >>
> > >> I want to simulate a peptide in water. The peptide has a formyl residue
>as the
> > >> N-terminus. I got the parameters of it and then add it to the .rtp file
>of
> > >> charmm36.ff as below:
> > >>
> > >> [ For ]
> > >> [ atoms ]
> > >> ; name type charge chargegroup
> > >> C C 0.4500 0
> > >> O O -0.5700 0
> > >> [ bonds ]
> > >> ; ai aj fu b0 kb, b0 kb
> > >> 1 2 1 0.12220 779866.6 0.12220 779866.6
> > >>
> > >> [ pairs ]
> > >> ; ai aj fu
> > >>
> > >> [ angles ]
> > >> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
> > >> 2 1 3 1 123.4390 403.48 123.4390 403.48
> > >> 2 1 4 1 123.4390 403.48 123.4390 403.48
> > >>
> > >> [ dihedrals ]
> > >> ; ai aj ak al fu phi0 kphi mult phi0 kphi mult
> > >>
> > >> But when I do what I described, I face this fatal error:
> > >> Fatal error:
> > >> No atoms found in .rtp file in residue pairs
> > >>
> > >> Would you help me with this problem? Did I add the formyl in a wrong
>way?
> > >>
> > >
> > > Your [pairs] directive is empty, hence the error. Your [dihedrals]
>directive
> > > will also produce the same error. There are no possible pairs in a unit
> > > containing so few atoms, so you don't even need this. You may need to
>define
> > > dihedrals, however, but they also depend upon the next residue.
> > >
> > > You also have several other mistakes:
> > >
> > > 1. A formyl group has a proton on it; yours has none
> > > 2. Your net charge on the formyl group is not zero, though this may or
>may not
> > > be a consequence of point #1
> > > 3. There is no connectivity information for linking to the next residue,
>which
> > > will mean the formyl group will not be chemically bonded. This also
>affects
> your
> > > dihedrals.
> > >
> >
> > Another that I just caught as I hit send:
> >
> > 4. In your [bonds] and [angles] directives, you use atom numbers - they
>should
> > be names
> >
> > -Justin
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul, Ph.D.
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
> > gmx-users mailing list gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
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>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> 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 gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
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>
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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