[gmx-users] Re: Re: Need favour

[Derrick Guang Yuh Lee]

Dear Poornima,

The first thing I will say is that I do recommend that you post these
messages to the GROMACS userlist, as others like yourself may be searching
for the exact same problems and other members more experienced than myself
would be available to answer your questions.

As for your problems with GROMACS failing, because the .top file you sent
me is incomplete, you did not list the number of DPPC or SOL molecules in
your system and I have no idea how many amino acids exist in your protein,
what I tell you from here on in is speculation.

 - The reason you are getting a non-zero charge of -9.99 is because you're
protein has a negative charge, more than likely due to high numbers of ASP
or GLU residues. You can compensate for this by using something like
genion to add in cations like Na or Ca.

 - The fatal error is simply because the number of atoms in your .top file
does not correspond to the number of atoms in your .gro file. You have to
open up your .gro file and figure out the exact number of DPPC and SOL
molecules you have and tose them into your .top file. Your current .top
file has too many atoms, 33935, vs. the actual number in your .gro file,
29435, and so you have an extra 4500 molecules added in. I'm assuming that
when you added your protein to the system, you had to remove DPPC lipids
and SOL molecules to insert the protein, when you do that, you must remove
those exact numbers from the .top file else GROMACS thinks that they
are there and hence you get that fatal error.

I hope this helps. Cheers.


Sincerely

 - Derrick Lee


 Derrick Guang Yuh Lee
 Department of Mathematics and Statistics / Department of Biochemistry
 Memorial University of Newfoundland
 k24dgyl at mun.ca / derrickglee at hotmail.com

"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
catalyst."
                                                              - bruce lee

On Wed, 21 Dec 2005, Poornima Gajendrarao wrote:

>   
Dear Sir,


Thank you  very much for you reply.. I tried without lipid.itp(from Tielemen's website). Its giving the following error.


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 1174 of the 2016 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 3 bonded neighbours for DPPC 128
Excluding 2 bonded neighbours for SOL 3655
Excluding 2 bonded neighbours for SOL 4383
WARNING 1 [file "dppc.top", line 24]:
  System has non-zero total charge: -9.999986e+00

processing coordinates...
Fatal error: number of coordinates in coordinate file (b4em.gro, 29435)
             does not match topology (dppc.top, 33935)


And I have sent my main *.top file with this mail.. Please try it out.
Waiting for your reply.

Thanking you in advance,

with Prayers,
Poornima





On Tue, 20 Dec 2005 Derrick Guang Yuh Lee wrote :
>Dear Poornima,
>
>The "second defaults directive" relates to two sets of forcefields
>conflicting with one another. I assume that in your .top file, you have
>listed ffgmx.itp, lipid.itp, and another forcefield for your specific
>lipid type (i.e. dppc.itp, popg.itp, etc). In my experience, Tieleman's
>lipid.itp was created for the older versions of GROMACS because when I
>excluded the lipid.itp file from my .top file, it works fine. If this
>doesn't work, send me a copy of your .top file and we'll look at it in a
>bit more detail. Cheers.
>
>
>
>Sincerely
>
>  - Derrick Lee
>
>
>  Derrick Guang Yuh Lee
>  Department of Mathematics and Statistics / Department of Biochemistry
>  Memorial University of Newfoundland
>  k24dgyl at mun.ca / derrickglee at hotmail.com
>
>"a teacher is never a giver of truth - he is a guide, a pointer to the
>truth that each student must find for himself. a good teacher is merely a
>catalyst."
>                                                               - bruce lee
>
>On Tue, 20 Dec 2005, Poornima Gajendrarao wrote:
>
> > Hai
>
>I am Poornima. I am new to Gromacs. I have to do lipid simulation. I am trying to do the simulation but during grompp program I am getting the following error message:
>
>
>
>creating statusfile for 1 node...
>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16#
>checking input for internal consistency...
>calling /lib/cpp...
>processing topology...
>Cleaning up temporary file gromppQQr7Ja
>Fatal error: Found a second defaults directive, file "lipid.itp", line 9
>
>When I searched the gromacs achieves I got that you too had the same problem and hope you will help to solve my problem..
>
>
>I have downloaded my Lipid files from the same website:
>
>Dr. Peter Tielemanhttp://moose.bio.ucalgary.ca/
>
>what to do? where to change?
>
>Can you help me to solve my problem?
>
>Thanking you in advance,
>
>With prayers
>Poornima
>
>