Dear Tsjerk,<br><br><blockquote style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;" class="gmail_quote">Hi Ahmet,<br><br>
As suggested, it's better to break up your molecule into smaller<br>
charge groups. Note that charge groups don't need to have zero charge,<br>
nor integer charge. In your case, I'd suggest two COH groups for EDO,<br>
which will have zero net charge each, and for TRS I'd take the COH<br>
groups as separate charge groups. I also note that the COH groups,<br>
although chemically identical - H3NC(COH)3, right?-, have different<br>
charges. That doesn't seem proper.<br><br>
Hope it helps,<br><br>
Tsjerk<br></blockquote>
<br>nonrevised .itp file:<br>EDO 3<br><br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br> 1 OA 1 EDO OAB 1 -0.111 15.9994 <br> 2 H 1 EDO HAE 1 0.031 1.0080 <br>
3 CH2 1 EDO CAA 1 0.080 14.0270 <br> 4 CH2 1 EDO CAC 1 0.080 14.0270 <br> 5 OA 1 EDO OAD 1 -0.111 15.9994 <br> 6 H 1 EDO HAF 1 0.031 1.0080 <br>
<br>nonrevised .itp file:<br>EDO 3<br><br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br> 1 OA 1 EDO OAB 1 -0.111 15.9994 <br> 2 H 1 EDO HAE 1 0.031 1.0080 <br>
3 CH2 1 EDO CAA 1 <b>0.000</b> 14.0270 <br> 4 CH2 1 EDO CAC 1 <b>0.000</b> 14.0270 <br> 5 OA 1 EDO OAD 1 -0.111 15.9994 <br> 6 H 1 EDO HAF 1 0.031 1.0080 <br>
<br>can you show me on the itp file? how do I seperate two COH groups? Please help me<br><br><div class="gmail_quote">31 Mart 2011 12:10 tarihinde Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> yazdż:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hi Ahmet,<br>
<br>
Why would I get angry? :) Sending a reply to the list will not usually<br>
be taken as asking for private tutoring...<br>
<br>
As Mark pointed out, you need to get familiar with the format of the<br>
files. That's the first thing you should do if you get to the point of<br>
needing to use non standard topologies. Read the manual, look at<br>
existing files. As for the immediate question, under the [ atoms ]<br>
section is a line indicating which column denotes what. You'd need to<br>
modify the columns 'cgnr' (charge group number) and probably 'charge'.<br>
For finding proper charge groups, in general you best draw your<br>
molecule, with the charges added, and then see which atoms would<br>
almost naturally group together.<br>
<div class="im"><br>
TRS.itp:<br>
..<br>
[ moleculetype ]<br>
; Name nrexcl<br>
TRS 3<br>
<br>
[ atoms ]<br>
; nr type resnr resid atom cgnr charge mass<br>
1 OA 1 TRS O1 1 -0.119 15.9994<br>
2 H 1 TRS H13 1 0.032 1.0080<br>
3 CH2 1 TRS C1 1 0.087 14.0270<br>
4 CCl4 1 TRS C 2 0.055 12.0110<br>
5 CH2 1 TRS C3 2 0.049 14.0270<br>
6 OA 1 TRS O3 2 -0.205 15.9994<br>
<br>
</div><div class="im">Hope it helps,<br>
<br>
Tsjerk<br>
<br>
<br>
<br>
2011/3/31 ahmet yżldżrżm <<a href="mailto:ahmedo047@gmail.com">ahmedo047@gmail.com</a>>:<br>
</div><div><div></div><div class="h5">> Dear Tsjerk,<br>
><br>
> I will ask you one thing but please do not get angry (I know you are not a<br>
> private tutor but I need your helps).<br>
><br>
> How do I apply on the files (EDO.itp and TRS.itp) that you said? (or can you<br>
> suggest a tutorial?)<br>
><br>
> Thanks<br>
><br>
> 2011/3/31 Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
>><br>
>> On 31/03/2011 5:18 PM, ahmet yżldżrżm wrote:<br>
>><br>
>> Dear users,<br>
>><br>
>> Before energy minimization step , I performed the preprosessing step using<br>
>> grompp .<br>
>> However, there are two note that :<br>
>><br>
>> NOTE 1 [file topol.top, line 52]:<br>
>> System has non-zero total charge: -1.500000e+01<br>
>><br>
>> This is an integer. See<br>
>> <a href="http://en.wikipedia.org/wiki/Scientific_notation#E_notation" target="_blank">http://en.wikipedia.org/wiki/Scientific_notation#E_notation</a> and<br>
>> <a href="http://www.gromacs.org/Documentation/Floating_Point_Arithmetic" target="_blank">http://www.gromacs.org/Documentation/Floating_Point_Arithmetic</a><br>
>><br>
>> NOTE 2 [file topol.top]:<br>
>> The largest charge group contains 11 atoms.<br>
>> Since atoms only see each other when the centers of geometry of the<br>
>> charge<br>
>> groups they belong to are within the cut-off distance, too large charge<br>
>> groups can lead to serious cut-off artifacts.<br>
>> For efficiency and accuracy, charge group should consist of a few atoms.<br>
>> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br>
>><br>
>> See Tsjerk's email.<br>
>><br>
>> Mark<br>
>><br>
>><br>
>> PS: TRS and EDO are not aminoacid<br>
>><br>
>> TRS.itp:<br>
>> ..<br>
>> [ moleculetype ]<br>
>> ; Name nrexcl<br>
>> TRS 3<br>
>><br>
>> [ atoms ]<br>
>> ; nr type resnr resid atom cgnr charge mass<br>
>> 1 OA 1 TRS O1 1 -0.119 15.9994<br>
>> 2 H 1 TRS H13 1 0.032 1.0080<br>
>> 3 CH2 1 TRS C1 1 0.087 14.0270<br>
>> 4 CCl4 1 TRS C 2 0.055 12.0110<br>
>> 5 CH2 1 TRS C3 2 0.049 14.0270<br>
>> 6 OA 1 TRS O3 2 -0.205 15.9994<br>
>> 7 H 1 TRS H33 2 0.019 1.0080<br>
>> 8 NL 1 TRS N 2 0.206 14.0067<br>
>> 9 H 1 TRS H2 2 0.004 1.0080<br>
>> 10 H 1 TRS H3 2 0.004 1.0080<br>
>> 11 H 1 TRS H1 2 0.004 1.0080<br>
>> 12 CH2 1 TRS C2 2 0.050 14.0270<br>
>> 13 OA 1 TRS O2 2 -0.205 15.9994<br>
>> 14 H 1 TRS H23 2 0.019 1.0080<br>
>> ...<br>
>><br>
>> EDO.itp<br>
>> ...<br>
>> [ moleculetype ]<br>
>> ; Name nrexcl<br>
>> EDO 3<br>
>><br>
>> [ atoms ]<br>
>> ; nr type resnr resid atom cgnr charge mass<br>
>> 1 OA 1 EDO OAB 1 -0.111 15.9994<br>
>> 2 H 1 EDO HAE 1 0.031 1.0080<br>
>> 3 CH2 1 EDO CAA 1 0.080 14.0270<br>
>> 4 CH2 1 EDO CAC 1 0.080 14.0270<br>
>> 5 OA 1 EDO OAD 1 -0.111 15.9994<br>
>> 6 H 1 EDO HAF 1 0.031 1.0080<br>
>> ...<br>
>><br>
>> topol.top:<br>
>> ..<br>
>> ; Include water topology<br>
>> #include "gromos43a1.ff/spc.itp"<br>
>> #include "TRS.itp"<br>
>> #include "EDO.itp"<br>
>> ..<br>
>> [ molecules ]<br>
>> ; Compound #mols<br>
>> Protein_chain_A 1<br>
>> Protein_chain_B 1<br>
>> SOL 185<br>
>> SOL 143<br>
>> TRS 1<br>
>> EDO 1<br>
>> SOL 44125<br>
>><br>
>> Conf.gro:<br>
>> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE<br>
>> 5354<br>
>> 2GLN N 1 1.458 -1.158 0.739<br>
>> 2GLN H1 2 1.520 -1.083 0.763<br>
>> .......<br>
>> 485HOH HW1 5333 0.221 -3.864 -2.291<br>
>> 485HOH HW2 5334 0.303 -3.946 -2.407<br>
>> 1TRS O1 1 -3.812 -0.471 -2.002<br>
>> 1TRS H13 2 -3.865 -0.443 -1.922<br>
>> 1TRS C1 3 -3.672 -0.469 -1.971<br>
>> 1TRS C 4 -3.635 -0.571 -1.863<br>
>> 1TRS C3 5 -3.711 -0.547 -1.731<br>
>> 1TRS O3 6 -3.694 -0.414 -1.679<br>
>> 1TRS H33 7 -3.746 -0.404 -1.594<br>
>> 1TRS N 8 -3.673 -0.705 -1.911<br>
>> 1TRS H2 9 -3.625 -0.725 -1.996<br>
>> 1TRS H3 10 -3.771 -0.707 -1.927<br>
>> 1TRS H1 11 -3.649 -0.774 -1.842<br>
>> 1TRS C2 12 -3.483 -0.573 -1.840<br>
>> 1TRS O2 13 -3.428 -0.445 -1.806<br>
>> 1TRS H23 14 -3.470 -0.412 -1.722<br>
>> 1EDO OAB 1 0.307 -2.792 0.149<br>
>> 1EDO HAE 2 0.390 -2.826 0.104<br>
>> 1EDO CAA 3 0.239 -2.901 0.212<br>
>> 1EDO CAC 4 0.111 -2.851 0.281<br>
>> 1EDO OAD 5 0.144 -2.763 0.388<br>
>> 1EDO HAF 6 0.060 -2.731 0.432<br>
>> 8.13100 7.04165 13.54850 0.00000 0.00000 -4.06550 0.00000<br>
>> 0.00000 0.00000<br>
>><br>
>> How can I fixed these notes(note 1 and note 2)?<br>
>><br>
>> Thanks in advance<br>
>> --<br>
>> Ahmet YILDIRIM<br>
>><br>
>><br>
>> --<br>
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><br>
><br>
><br>
> --<br>
> Ahmet YILDIRIM<br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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><br>
<br>
<br>
<br>
--<br>
</div></div><div class="im">Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
</div>--<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>