[gmx-users] problem regarding do_dssp

[Yang Ye]

do_dssp calls external dssp program to do the calculation which is slow 
but shall not take "lot of time"
. For fast execution of DSSP, you may consider using my_dssp.

Go to your gromacs source directory:
./configure
make
cd src/contrib
make my_dssp

Regards,
Yang Ye

On 2/7/2007 5:41 PM, sangeeta wrote:
> Dear Mark, 
>
>    Previously you suggested to try running dssp independently on a single 
> snapshot extracted from the trajectory,I took the snapshot of the protein 
> after 1ns with the command 
>
> trjconv -f md.xtc -s md.tpr -o time_1000ps.pdb -dump 1000
>
> then ran dssp program by using the command 
>
> dsspcmbi time_1000ps.pdb DSSPtime_1000ps.pdb 
>
>  The program ran successfully,but again when I used 
>  
> do_dssp -s md.tpr -f time_1000ps.pdb 
>   
> the program is taking lot of time.I do not understand where I am making the  
> mistake, please help and give me solution.Thanks in advance.
>
>
> regards
> SANGEEA
>
> On Mon, 5 Feb 2007 18:56:22 +1100 (EST), Mark Abraham wrote
>   
>>> Dear All,
>>>
>>>        I want to analyze the secondary structure of a protein after a 
>>>       
> 10ns
>   
>>> simulation run. Previously I faced difficulty in running dssp program,So
>>> in
>>> order to  give a test run I ran the do_dssp program  for  100ps
>>> trajectory
>>> only for  a protein containing 130 residues.The program continued for 
>>>       
> more
>   
>>> than 4 days, yet it was not completed, Only it was giving the 
>>>       
> intermediate
>   
>>> files namely ddEyzdyf,ddKDeKnT etc, except that no ouput were produced.I
>>> do
>>> not understand how long it will take or whether I am encountering any
>>> problem , in  the manual it is mentioned that the program is very slow,
>>> But
>>> I am not getting any idea whether the time it is taking  is normal, or I
>>> am
>>> facing some problem.
>>>       
>> Try doing it on one structure in a trajectory by using trjconv
>> appropriately. If it's not done in ten minutes on a machine under 
>> five years old, then you have a problem.
>>
>> Also try running dssp independently on a single snapshot extracted from
>> your trajeotry and put into pdb format (by specifying .pdb suffix on
>> output file for trjconv). If you can't do that, then the problem has
>> nothing to do with gromacs.
>>
>> Mark
>>
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>
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