[gmx-users] Fatal error: No atoms found in .rtp file in residue pairs
Mark Abraham
Mark.Abraham at anu.edu.au
Mon May 14 10:12:23 CEST 2012
On 14/05/2012 6:00 PM, Shima Arasteh wrote:
> Thanks for your suggestions.
> Now, I think that it's better to add the N atom of next residue to
> the .pdb file and then add hydrogen atoms to its .mol2 format. Because
> when I open formyl.pdb in chimera software and add hydrogens to it,
> it becomes an formaldehyde and then I get the a wrong parameters in
> .itp file by using SwissParam. So I didn't remove the N atom which
> connects to the C of formyl. Now I got this .itp file:
>
> ; nr type resnr resid atom cgnr charge mass
> 1 CR 1 LIG C 1 0.5500 12.0110
> 2 OR 1 LIG O 2 -0.6800 15.9994
> 3 HCMM 1 LIG H4 3 0.0000 1.0079
> 4 HCMM 1 LIG H6 4 0.0000 1.0079
> 5 HOR 1 LIG H8 5 0.4000 1.0079
> 6 NR 1 LIG N 6 -0.9900 14.0067
> 7 HNR 1 LIG H2 7 0.3600 1.0079
> 8 HNR 1 LIG H1 8 0.3600 1.0079
>
> Would this file work probably? I mean can I get the correct parameters?
Since you can't have a double bond with that many bonded hydrogen atoms
present, no.
Like Justin has suggested, one approach is to take the whole residue
adjacent to formyl and parameterise all of it. Another would be to take
the acetyl group for that force field and assign the total charge of the
methyl group to the hydrogen of your formyl - but this has obvious
shortcomings.
>
> The .rtp file which I arranged, is as below:
> [ For ]
> [ atoms ]
> ; name type charge chargegroup
> C CTL1 0.5500 0
> O O -0.6800 0
> H HC 0.1300 0
> [angles ]
> ai aj ak
> O C +N
> O C H
> H C +N
>
> [ bonds ]
> C O
> C +N
> C H
>
> [ dihedrals ]
> O C +N +CA
> H C +N +H
> H C +N +H
>
> Would it be correct? I got the charge of H atom by assuming the total
> charge of formyl is zero.
Only if you think the carbonyl group forming an amide bond consists only
of atoms with equivalent electronegativity. Any model that does not have
partial negative charge on the oxygen will be not worth the time to
write down.
Mark
>
>
>
>
>
> Sincerely,
> Shima
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at 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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at 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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
> > > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> > <mailto:gmx-users at gromacs.org <mailto:gmx-users at 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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