Fw: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs
Shima Arasteh
shima_arasteh2001 at yahoo.com
Mon May 14 11:20:25 CEST 2012
Thanks for your suggestions.
Now I got the .itp file for frmyl+valine(the next residue).
This is the .itp file got from the SwissParam.
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 C=O 1 LIG C 1 0.5700 12.0110
2 O=C 1 LIG O 2 -0.5700 15.9994
3 NC=O 1 LIG N 3 -0.7301 14.0067
4 CR 1 LIG CA 4 0.1941 12.0110
5 CO2M 1 LIG C1 5 0.9060 12.0110
6 O2CM 1 LIG O1 6 -0.9000 15.9994
7 CR 1 LIG CB 7 0.0000 12.0110
8 CR 1 LIG CG1 8 0.0000 12.0110
9 CR 1 LIG CG2 9 0.0000 12.0110
10 O2CM 1 LIG OXT 10 -0.9000 15.9994
11 HCMM 1 LIG H 11 0.0600 1.0079
12 HNCO 1 LIG H1 12 0.3700 1.0079
13 HCMM 1 LIG HA 13 0.0000 1.0079
14 HCMM 1 LIG HB 14 0.0000 1.0079
15 HCMM 1 LIG HG11 15 0.0000 1.0079
16 HCMM 1 LIG HG12 16 0.0000 1.0079
17 HCMM 1 LIG HG13 17 0.0000 1.0079
18 HCMM 1 LIG HG21 18 0.0000 1.0079
19 HCMM 1 LIG HG22 19 0.0000 1.0079
20 HCMM 1 LIG HG23 20 0.0000 1.0079
Now I made this .rtp file as below:
[ For ]
[ atoms ]
; name type charge chargegroup
C CTL1 0.5700 0
O O -0.5700 0
H HC 0.06 0
[angles ]
ai aj ak
O C +N
O C H
O
C +N
[ bonds ]
C O
C +N
C H
[ dihedrals ]
O C +N +CA
H C +N +H
H C +N +H
You
know, actually I want to get a correct .itp file to use it later the
parameters later if it is needed. would you suggest me about this file?
Sincerely,
Shima
________________________________
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, May 14, 2012 12:42 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs
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>
>> *To:* Discussion list for GROMACS users <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>>
>> > *To:* Discussion list for GROMACS users <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
>>
>>
>
>
>
>
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