I have updated the .top file as well after removing all the overlapping lipids from .gro file<br><br><div class="gmail_quote">On Thu, Jan 14, 2010 at 10:15 AM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Probably you removed lipids from the gro but not from the top (which you need to do as well).<br>
<br>
Find a lipid atom name that occurs only once per molecule (In non-united atom lipids I use P8)<br>
<br>
grep P8 my.gro |wc -l<br>
<br>
This will tell you how many lipids should appear in your top file.<br>
<br>
Chris.<br>
<br>
-- original message --<br>
<br>
Hi All,<br>
<br>
I am running simulation of a system containing Coarse Grained 1SU4<br>
(Minimized structure) and Coarse Grained DPPC lipid. I used the INFLATEGRO<br>
script to inflate the lipid and removed the overlapping lipids with proteins<br>
and then running the energy minimization.<br>
<br>
grommp says there are mismatching of atoms in system.top file (which<br>
consists of DPPC, Protein and W) and inflated_bilayer.gro (Which Inflategro<br>
script developed). I don't know why this is happening and why the atoms are<br>
not matching. Also, is there any problem with the atom2cg.awk script which<br>
MARTINI guys provided or they have any other script which converts the<br>
atomic structure of protein to CG protein so that at the time of simulation<br>
the atoms match.<br>
<br>
I am using the grompp command something like this.<br>
<br>
grompp -f em.mdp -c inflated_bilayer.gro -p system.top -maxwarn 10<br>
<br>
grompp says: atom name 1 in system.top and inflated_bilayer.gro does not<br>
match (NC3-BCQd)<br>
<br>
and it keeps on going until 2116 atoms.<br>
<br>
I dnt know how to fix this. Reply will be appreciable.<br>
<br>
Thanks,<br>
<br>
Sunny<br>
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