Dear Tsjerk,
Hi Ahmet,
>
> As suggested, it's better to break up your molecule into smaller
> charge groups. Note that charge groups don't need to have zero charge,
> nor integer charge. In your case, I'd suggest two COH groups for EDO,
> which will have zero net charge each, and for TRS I'd take the COH
> groups as separate charge groups. I also note that the COH groups,
> although chemically identical - H3NC(COH)3, right?-, have different
> charges. That doesn't seem proper.
>
> Hope it helps,
>
> Tsjerk
>
nonrevised .itp file:
EDO 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 EDO OAB 1 -0.111 15.9994
2 H 1 EDO HAE 1 0.031 1.0080
3 CH2 1 EDO CAA 1 0.080 14.0270
4 CH2 1 EDO CAC 1 0.080 14.0270
5 OA 1 EDO OAD 1 -0.111 15.9994
6 H 1 EDO HAF 1 0.031 1.0080
nonrevised .itp file:
EDO 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 EDO OAB 1 -0.111 15.9994
2 H 1 EDO HAE 1 0.031 1.0080
3 CH2 1 EDO CAA 1 *0.000* 14.0270
4 CH2 1 EDO CAC 1 *0.000* 14.0270
5 OA 1 EDO OAD 1 -0.111 15.9994
6 H 1 EDO HAF 1 0.031 1.0080
can you show me on the itp file? how do I seperate two COH groups? Please
help me
31 Mart 2011 12:10 tarihinde Tsjerk Wassenaar <tsje...@gmail.com> yazdı:
> Hi Ahmet,
>
> Why would I get angry? :) Sending a reply to the list will not usually
> be taken as asking for private tutoring...
>
> As Mark pointed out, you need to get familiar with the format of the
> files. That's the first thing you should do if you get to the point of
> needing to use non standard topologies. Read the manual, look at
> existing files. As for the immediate question, under the [ atoms ]
> section is a line indicating which column denotes what. You'd need to
> modify the columns 'cgnr' (charge group number) and probably 'charge'.
> For finding proper charge groups, in general you best draw your
> molecule, with the charges added, and then see which atoms would
> almost naturally group together.
>
> TRS.itp:
> ..
> [ moleculetype ]
> ; Name nrexcl
> TRS 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 OA 1 TRS O1 1 -0.119 15.9994
> 2 H 1 TRS H13 1 0.032 1.0080
> 3 CH2 1 TRS C1 1 0.087 14.0270
> 4 CCl4 1 TRS C 2 0.055 12.0110
> 5 CH2 1 TRS C3 2 0.049 14.0270
> 6 OA 1 TRS O3 2 -0.205 15.9994
>
> Hope it helps,
>
> Tsjerk
>
>
>
> 2011/3/31 ahmet yıldırım <ahmedo...@gmail.com>:
> > Dear Tsjerk,
> >
> > I will ask you one thing but please do not get angry (I know you are not
> a
> > private tutor but I need your helps).
> >
> > How do I apply on the files (EDO.itp and TRS.itp) that you said? (or can
> you
> > suggest a tutorial?)
> >
> > Thanks
> >
> > 2011/3/31 Mark Abraham <mark.abra...@anu.edu.au>
> >>
> >> On 31/03/2011 5:18 PM, ahmet yıldırım wrote:
> >>
> >> Dear users,
> >>
> >> Before energy minimization step , I performed the preprosessing step
> using
> >> grompp .
> >> However, there are two note that :
> >>
> >> NOTE 1 [file topol.top, line 52]:
> >> System has non-zero total charge: -1.500000e+01
> >>
> >> This is an integer. See
> >> http://en.wikipedia.org/wiki/Scientific_notation#E_notation and
> >> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> >>
> >> NOTE 2 [file topol.top]:
> >> The largest charge group contains 11 atoms.
> >> Since atoms only see each other when the centers of geometry of the
> >> charge
> >> groups they belong to are within the cut-off distance, too large
> charge
> >> groups can lead to serious cut-off artifacts.
> >> For efficiency and accuracy, charge group should consist of a few
> atoms.
> >> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO,
> etc.
> >>
> >> See Tsjerk's email.
> >>
> >> Mark
> >>
> >>
> >> PS: TRS and EDO are not aminoacid
> >>
> >> TRS.itp:
> >> ..
> >> [ moleculetype ]
> >> ; Name nrexcl
> >> TRS 3
> >>
> >> [ atoms ]
> >> ; nr type resnr resid atom cgnr charge mass
> >> 1 OA 1 TRS O1 1 -0.119 15.9994
> >> 2 H 1 TRS H13 1 0.032 1.0080
> >> 3 CH2 1 TRS C1 1 0.087 14.0270
> >> 4 CCl4 1 TRS C 2 0.055 12.0110
> >> 5 CH2 1 TRS C3 2 0.049 14.0270
> >> 6 OA 1 TRS O3 2 -0.205 15.9994
> >> 7 H 1 TRS H33 2 0.019 1.0080
> >> 8 NL 1 TRS N 2 0.206 14.0067
> >> 9 H 1 TRS H2 2 0.004 1.0080
> >> 10 H 1 TRS H3 2 0.004 1.0080
> >> 11 H 1 TRS H1 2 0.004 1.0080
> >> 12 CH2 1 TRS C2 2 0.050 14.0270
> >> 13 OA 1 TRS O2 2 -0.205 15.9994
> >> 14 H 1 TRS H23 2 0.019 1.0080
> >> ...
> >>
> >> EDO.itp
> >> ...
> >> [ moleculetype ]
> >> ; Name nrexcl
> >> EDO 3
> >>
> >> [ atoms ]
> >> ; nr type resnr resid atom cgnr charge mass
> >> 1 OA 1 EDO OAB 1 -0.111 15.9994
> >> 2 H 1 EDO HAE 1 0.031 1.0080
> >> 3 CH2 1 EDO CAA 1 0.080 14.0270
> >> 4 CH2 1 EDO CAC 1 0.080 14.0270
> >> 5 OA 1 EDO OAD 1 -0.111 15.9994
> >> 6 H 1 EDO HAF 1 0.031 1.0080
> >> ...
> >>
> >> topol.top:
> >> ..
> >> ; Include water topology
> >> #include "gromos43a1.ff/spc.itp"
> >> #include "TRS.itp"
> >> #include "EDO.itp"
> >> ..
> >> [ molecules ]
> >> ; Compound #mols
> >> Protein_chain_A 1
> >> Protein_chain_B 1
> >> SOL 185
> >> SOL 143
> >> TRS 1
> >> EDO 1
> >> SOL 44125
> >>
> >> Conf.gro:
> >> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
> >> 5354
> >> 2GLN N 1 1.458 -1.158 0.739
> >> 2GLN H1 2 1.520 -1.083 0.763
> >> .......
> >> 485HOH HW1 5333 0.221 -3.864 -2.291
> >> 485HOH HW2 5334 0.303 -3.946 -2.407
> >> 1TRS O1 1 -3.812 -0.471 -2.002
> >> 1TRS H13 2 -3.865 -0.443 -1.922
> >> 1TRS C1 3 -3.672 -0.469 -1.971
> >> 1TRS C 4 -3.635 -0.571 -1.863
> >> 1TRS C3 5 -3.711 -0.547 -1.731
> >> 1TRS O3 6 -3.694 -0.414 -1.679
> >> 1TRS H33 7 -3.746 -0.404 -1.594
> >> 1TRS N 8 -3.673 -0.705 -1.911
> >> 1TRS H2 9 -3.625 -0.725 -1.996
> >> 1TRS H3 10 -3.771 -0.707 -1.927
> >> 1TRS H1 11 -3.649 -0.774 -1.842
> >> 1TRS C2 12 -3.483 -0.573 -1.840
> >> 1TRS O2 13 -3.428 -0.445 -1.806
> >> 1TRS H23 14 -3.470 -0.412 -1.722
> >> 1EDO OAB 1 0.307 -2.792 0.149
> >> 1EDO HAE 2 0.390 -2.826 0.104
> >> 1EDO CAA 3 0.239 -2.901 0.212
> >> 1EDO CAC 4 0.111 -2.851 0.281
> >> 1EDO OAD 5 0.144 -2.763 0.388
> >> 1EDO HAF 6 0.060 -2.731 0.432
> >> 8.13100 7.04165 13.54850 0.00000 0.00000 -4.06550 0.00000
> >> 0.00000 0.00000
> >>
> >> How can I fixed these notes(note 1 and note 2)?
> >>
> >> Thanks in advance
> >> --
> >> Ahmet YILDIRIM
> >>
> >>
> >> --
> >> gmx-users mailing list gmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
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> >
> >
> >
> > --
> > Ahmet YILDIRIM
> >
> > --
> > gmx-users mailing list gmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>
--
Ahmet YILDIRIM
--
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