[gmx-users] Re: about hp.mdp again!!!

[Graham Smith]

nanyu101 wrote: 

> I have made a hole in POPC128a bilayer.But I failed inputing protein
> into it.Am I hp.mdp file right?

I think so. 

> I have already run these.
> genconf -f insert.gro -o insert.pdb

I dont know what your protein is called so I'll call it pr.pdb
do 

editconf -f insert.gro -o insert.pdb 
cat pr.pdb insert.pdb > pr_and_lipid.pdb 

(you will have to edit pr_and_lipid.pdb by hand to move the
HEADER  
REMARK    THIS IS A SIMULATION BOX
CRYST1  ...
lines which will be in the middle (from insert.pdb) to the start;
you should probably remove MODEL and ENDMDL lines too. 

Then look at it with your pdb viewer. If all has gone well the
protein should lie in the hole that was made in the insert.pdb
file. 

To do more MD you'll have to make a new topology for the combined
system; run pdb2gmx on pr.pdb if you haven't already, which will make
a new pr.top file, then combine this by hand with your popc.top. 

Graham 

######################################################################

Dr. Graham R. Smith,
Biomolecular Modelling Laboratory,
Cancer Research UK,
44 Lincoln's Inn Fields,
London WC2A 3PX,
U.K.
Tel: +44-(0)20 7269 3348
email: graham.smith at cancer.org.uk
URL: http://www.bmm.icnet.uk/~smithgr