Sincerely,
Shima
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Sent:* Sunday, May 13, 2012 9:40 PM
*Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in
residue pairs
On 5/13/12 12:42 PM, Shima Arasteh wrote:
> OK, so I entered the H atom corresponding to the structure and then
changed the
> file as below,
>
> [ For ]
> [ atoms ]
> ; name type charge charge group
> C CTL1 0.5700 0
> O O -0.5700 0
> H HC 0.00 0
>
I find it highly unlikely that a zero charge should be assigned to
this proton.
The .itp file you posted before from SwissParam was for
formaldehyde, which
suggests to me you haven't properly parameterized the species you're
looking for
and now you're trying to hack something together. Don't try to do
that; your
parameters will be junk. Parameterize the right species once and
proceed from
there.
> [angles ]
> ai aj ak
> O C +N
> O C H
>
> [ bonds ]
> C O
> C +N
> C H
>
> [ dihedrals ]
> O C +N +CA
> H C +N +H
>
There are other possible dihedrals here.
-Justin
>
>
>
--------------------------------------------------------------------------------
> *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:* 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>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
> > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
> <mailto: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> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>>
> > 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 gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
> <mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
> > <mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
>
> --
> ========================================
>
> 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> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
> 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 gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
> <mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
--
========================================
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>
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 gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
