Dear users,<br><br>Firstly thanks for your replies. I have two ligands <span id="result_box" class="short_text" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps">as I said</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">before</span></span>.<br>
I will analyze the system together ligands after the simulation is finished.<br>For example:<br>I want to plot potential energy of all system (that is, protein+LİGA+LİGB) by g_energy.<br>Then, <br>Should I create the groups as the following?<br>
<br><b>energygrps = Protein LİGA_LİGB</b><br>tc-grps = Protein_LİGA_LİGB Water_and_ions<br><br>OR<br><br><b>energygrps = Protein LİGA LİGB</b><br>
tc-grps = Protein_LİGA_LİGB Water_and_ions<br><br>Thanks<br><br><div class="gmail_quote">12 Mayıs 2011 18:29 tarihinde lina <span dir="ltr"><<a href="mailto:lina.lastname@gmail.com">lina.lastname@gmail.com</a>></span> yazdı:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">2011/5/12 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>:<br>
<div class="im">><br>
><br>
> lina wrote:<br>
>><br>
>> make_ndx -f your.gro/pdb -n your.ndx -o your.ndx<br>
>><br>
>> LiGA & LİGB:<br>
><br>
> This is not correct. You need to use | rather than &. Using logical and<br>
> (&) means the index group will contain atoms that are common to both LIGA<br>
> and LIGB. If they are distinct entities, the group will be empty. Logical<br>
> or (|) says merge the two different groups to create one unified group.<br>
<br>
</div>Ooops<br>
<div><div></div><div class="h5"><br>
<br>
><br>
> -Justin<br>
><br>
>> q<br>
>><br>
>> in grompp add -n your.ndx<br>
>><br>
>><br>
>> 2011/5/12 ahmet yıldırım <<a href="mailto:ahmedo047@gmail.com">ahmedo047@gmail.com</a>>:<br>
>>><br>
>>> Dear users,<br>
>>><br>
>>> I have two ligands. I created a special index group that merges the<br>
>>> protein,<br>
>>> LiGA and LİGB.<br>
>>><br>
>>> I have the pr.mdp file as the following:<br>
>>> ...<br>
>>> energygrps = Protein LİGA_LİGB<br>
>>> tc-grps = Protein_LİGA_LİGB Water_and_ions<br>
>>> ...<br>
>>><br>
>>> grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr<br>
>>> Fatal error:<br>
>>> Group LİGA_LİGB not found in indexfile.<br>
>>><br>
>>> I get the fatal error since I dont have a special index group that merges<br>
>>> LiGA and LİGB. should I create two different index file?<br>
>>><br>
>>> Thanks in advance<br>
>>> --<br>
>>> Ahmet YILDIRIM<br>
>>><br>
>>> --<br>
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>>><br>
>><br>
>><br>
>><br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
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><br>
<br>
<br>
<br>
</div></div>--<br>
Best Regards,<br>
<br>
lina<br>
<font color="#888888">--<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>