[gmx-users] mdrun-hole Questions....

Senthil Kandasamy senthilk at engin.umich.edu
Tue Dec 24 17:07:21 CET 2002

Hi All,

I tried to use Graham Smiths's mdrun-hole package. Though his tutorial
is fairly comprehensive and I followed his procedure step by step, I did
not get the hole that I wanted. Let me explain what I did and hopefully
some one will be able to shed some light.

I am trying to insert one alpha-helical peptide halfway into the bilayer
(only one leaflet will be disturbed). (This must be fairly trivial when
compared to the more complex proteins that other people insert.)  I 
created  two pdbs, bilayer.pdb and  peptide.pdb . The peptide 
coordinates were adjusted using editconf to be at the desired vertical 
position in the bilayer.

I ran pdb2xyzr to get peptide xyzr values. Then, I ran msms to get the
face and vert files. So far so good.

Three lipids were clashing badly with the proposed protein cavity and
about seven other lipids had minor contacts. I removed the three lipids
from the bilayer.pdb. Since I am inserting the peptide only into one of
the leaflets, there is a lot of the peptide sticking out into the water.
I removed all the waters that were clashing with the  peptide. So, now
there are very few atoms in the cavity and they are all atoms from 7 
lipids partially present in the cavity  region.

Now, I am ready to run md-run-hole (which, I had installed separately,
in a different gromacs distribution than the main one). If I unserstand 
things correctly, it should drive out the lipids atoms in the peptide 
cavity leavin me with a nice hoel to insert the peptide into.

I ran grompp -f dppc-mdrun.mdp -p dppc.top - c bilayer-3lipids.pdb -o

I used a simple cut-off for vdw. Most of the other parameters were ones 
that I use for a generic mdrun.

now comes the acid test.

I ran mdrun-hole.

mdrun-hole -v -s insert-cavity.tpr -s insert-cavity.trr -c cavity.gro 
-hole   -holep hp.mdp.

I tried to keep as simple an mdp file as possible.
(May be I am doing something wrong here)
Here is my hp.mdp

> holetype                 = MSMS
> hfm                      = 50
> supf                     = 20
> molsurf_log              = gsurf.log 
> hp1 			   = 1
> hp2 			   = 12600   ; I have 252 DPPCs
> supf 			   = 50
> molsurf_file             = peptide
> debugsurf 		   = no 	
> resforces  		   = yes

running with debugsurf=yes gives two pdbs. the insidesurf.pdb seems to 
have about 25 atoms inside it which seems about right.

However, after running mdrun-hole for about 20 ps, I get a lot of water 
an lipids flowing into the hole.

I start with about 25 atoms to be pushed out, but end up with more than 
300 atoms in the cavity.

What am I doing wrong here? Do I need to add more paramters to the 
hp.mdp file? (for example, set hz values to add a z directed force? I 
assumed that it was unnecessary in my case.) May be run for much longer 
than 20 ps. That doesn't seem right...

Any help will be really appreciated.



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