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<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>Rhodopsin in membrane EM</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">I’m starting to use gromacs.<SPAN
style="mso-spacerun: yes"> </SPAN>At the beginning I wanted to do MD <SPAN
style="mso-spacerun: yes"> </SPAN>of rhodopsin in membrane.<SPAN
style="mso-spacerun: yes"> </SPAN>So at first, <SPAN
style="mso-spacerun: yes"> </SPAN>I preformed EM of rhodopsin in membrane
made of three different kinds of lipids.<SPAN style="mso-spacerun: yes">
</SPAN>(For coordinate file I used pdb file involving coordinates for whole
system: water, lipids and rhodopsin.<SPAN style="mso-spacerun: yes">
</SPAN>This pdb file is a coordinate output file from NAMD after MD simulation
and I guess it doesn’t have any errors).<SPAN style="mso-spacerun: yes">
</SPAN>My problem is that after EM using gromacs I got very strange
results.<SPAN style="mso-spacerun: yes"> </SPAN>In my output pdb file
lipids broke into small pieces and the chain of the protein had a lot of gaps.
<SPAN style="mso-spacerun: yes"> </SPAN>I used mdp file similar to this
from speptide tutorial.<SPAN style="mso-spacerun: yes"> </SPAN>Itp files
for lipids I did on my own, and itp file for protein I obtained using pdb2gmx.
<SPAN style="mso-spacerun: yes"> </SPAN>During the EM I did not have any
errors. <SPAN style="mso-spacerun: yes"> </SPAN>Maybe someone knows what
could be the problem. <SPAN style="mso-spacerun: yes"> </SPAN>Thank you in
advance.<SPAN style="mso-spacerun: yes"> </SPAN>Mike <?xml:namespace
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