But where exactly error in such inclussion ?<br><br>In G_membed manual I've found only this statement about inclussion of the ligands<br><br> When the group to embed is not a default group, such as a protein and its crystal water, an ndx file<br>
should also be provided to g membed. Make sure all the molecule types in the group to embed are unique,<br>e.g. the molecule type of the crystal waters should be different from that of the solvent. Also the freeze<br>and energy exclusion parameters in the mdp file should be changed to match the name of the group to<br>
embed.<br><br>This tell nothing how exactly define mdp file. The way that I've used gave me those strange error that pop ( membrane ) was in the first group wich really contained of only merged protein and ligand (2 different mol. types). This merging I've done by means of index_ndx based on the GRO file with I've provide to GROMPP.<br>
<br>Also I've tried to do it in another manner defining all groups separately<br><br>integrator = md<br>energygrps = Protein ADN<br>freezegrps = Protein ADN<br>freezedim = Y Y Y Y Y Y<br>energygrp_table<br>
energygrp_excl = Protein Protein<br><br>In that case I have no such problem but during insertion G_membed has deleted ADN.<br><br>James<br><br><br><br><div class="gmail_quote">2012/6/20 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">On 20/06/2012 5:08 PM, James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Mark,<br>
<br>
I've made changes in the input mdp file<br>
<br>
integrator = md<br>
energygrps = Protein_ADN<br>
freezegrps = Protein_ADN<br>
freezedim = Y Y Y<br>
energygrp_table<br>
energygrp_excl = Protein_ADN Protein_ADN<br>
<br>
here Protein_ADN is the protein_ligand defined in the index.mdp<br>
<br>
than I've processed by grompp without problems<br>
<br>
but during insertion step by follow command<br>
g_membed -f input.tpr -p topol.top -n index.ndx -xyinit 0.1 -xyend 1.0 -nxy 1000<br>
<br>
here I choose Protein_ADN as the group to be inserted and POP as the group wich are membrane. Eventually I've obtained another strange error<br>
<br>
Moleculetype POP is found both in the group to insert and the rest of the system.<br>
Because we need to exclude all interactions between the atoms in the group to<br>
insert, the same moleculetype can not be used in both groups. Change the<br>
moleculetype of the molecules POP in the inserted group.<br>
<br>
I've checked my index.ndx and didt not find POP group in my first Protein_ADN group. Why this error should be ?<br>
</blockquote>
<br></div>
Then it seems you're checking things that don't match each other. The numbers in the index file must relate to the whole system, defined by the [molecules] section. You need to make the index group from a file that corresponds to that section, i.e. from the coordinate file you give to grompp, which also must match that section. You should note also any particular requirements in the g_membed documentation about whether the insertion group has to be a single molecule or moleculetype.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="HOEnZb"><div class="h5"><br>
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