[gmx-developers] removal of water by keepbyz.pl script

[chris.neale at utoronto.ca]

Dear Tasneem:

Try reading through the material here:
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations

1. There are actually about 10 steps that you must follow to use this  
routine (see that web page listed above).

2. The C-program is *much* faster and does exactly the same thing, so  
I suggest that you compile keepbyz.c and use it instead.

3a. You need to modify the script or program depending on if you have  
velocities in your .gro file. This is outlines on that same webpage.

3b. You need to modify the bash script to let it know how many atoms  
are in your water model (but the C program takes this as command line  
input). This is outlines on that same webpage.

Chris.


Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> tasneem jahan wrote:
>> Hi,
>> I am trying to remove water from hydrophobic core of lipd for my   
>> membrane protein.
>> but whan I am using keepbyz.pl <http://keepbyz.pl> script it    
>> generate plain text file in  .gro  of not_last_line.gro.
>
> I don't understand what you mean.  A .gro file is a text file.
>
>> generate expr : syntax error.
>
> What command gives you this error?  Have you followed all the commands
> correctly?
>
> -Justin
>
>> please help me out how to fix it.
>> Thanks!
>>
>> -- tasneem Jahan
>> Project Trainee
>> C/o-Dr.Ajay K .Saxena
>> Structure Biology Lab
>> School Of Life Science
>> Jawaharlal Nehru University
>> New Delhi
>>
>
> -- 
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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