Hi Una,
That seems perfectly sensible. The only thing is that I'd use editconf
for renumbering, but I'm not even sure whether that will actually make
a difference.
Best,
Tsjerk
On 10/11/06, Una Bjarnadottir <[EMAIL PROTECTED]> wrote:
Thank you so much for your response Viswanadham Sridhara and Tsjerk
Wassenaar Still I seem to be doing something wrong because the ions
always end up in the active site cleft!. This is what I do: 1. I move
the 2 watermolecules (all three atoms) which I don't want to be replaced
at the bottom of the .gro file generated from genbox 2. Than I make
another .gro file using genconf to renumber the atoms 3. Make a .ndx
file from the renumbered .gro file and than delete the last 6 atoms from
the [SOL] group 4. Run genion after grompp using the .ndx file and
choose group [SOL] and a new .gro file is generated If you could comment
on this than that would be highly appreaciated. Best regards, Una you
might have deleted just one atom of water molecule. Ex: If you are using
SPC water , you have to delete all 3 atoms in index file. Best way is to
make changes in .gro file.. Renumber the resulting .gro file using
genconf, make a new index file and start running. On 10/10/06, Una
Bjarnadottir <[EMAIL PROTECTED]> wrote:
>>
>> Dear users,
>>
>> In some of my simulations after neutralizing the systems with genion 2
>> of the ions were inside the active site cleft of the protein.
>> In the discussion on the list it was commented to either delete the
>> solvent within the protein which I did I deleted the water molecule
>> (11798) and gave genion that index file as input but than this error came:
>>
>> Fatal error: The solvent group is not continuous: index[8198]=11797,
>> index[8199]=11799
>>
>> I don't want to use the -random command in genion if possible because in
>> none of the other simulations I have used it.
>>
>> Is there any other way to delete the solvent within the protein did I
>> misunderstand that so those water molecules will not be replaced?
>>
>> Best regards, Una Bjarnadottir
>
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--
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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