[gmx-users] Re: protein in popc

Graham Smith graham.smith at biiuk.com
Mon May 15 13:48:44 CEST 2006

> Message: 2
> Date: Mon, 15 May 2006 02:32:06 -0700 (PDT)
> From: mahbubeh zarrabi <zarrab_m at yahoo.com>
> Subject: [gmx-users] protein in popc
> To: gmx-users at gromacs.org
> Message-ID: <20060515093206.21682.qmail at web51605.mail.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
> dear freinds
> I have made a hole in POPC128a bilayer.But I failed
> inputing protein into it.I run below commands but
> there is not protein in the hole.whould you please
> help me? do you have another
>  protocol for protein insertion in popc (in detail)?
> make_hole.pl -f popc.pdb -o popcout.pdb -r 1.4 -lipat
> P8 -lipid POP -cx 2.3 -cy 2.8
> grompp -f run.mdp -o insert.tpr -c popcout.pdb -p
> popc.top
> mdrun -v -hole -holep hp.mdp -deffnm insert
> -----------------------------------------------------

Dear Mahbubeh,

I don't know if more up-to-date protocols have since been developed, I 
don't work on membrane proteins any more. However, if you still want to 
try to use the older hole-making code:
(a) you are using a special version of mdrun compiled from old gromacs 
version 3.1.4 and the extra code available from the contributions section
(b) you have looked at the html-format tutorial notes.
(c) "Hole-making" forces are being generated and applied to certain 
atoms: to see this, run with
debugsurf 		 = yes
in the hp.mdp files and it will stop at step 0 after producing extra 
pdbs with the dummy atoms to show the forces (see tutorial)
(d), Finally, the output of mdrun -v -hole -holep hp.mdp... will not 
have the protein inserted directly, but will just have a hole in the 
right place for your protein to be put in (by combining the pdb or gro 
files with an editor).

Dr Graham R. Smith
Head of Protein-Protein Interactions
Biosystems Informatics Institute
Newcastle upon Tyne

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