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>
*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
>
> ========================================
> --
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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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--
========================================
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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