[gmx-users] dssp works fine, but do_dssp gives fatal error

[Erik Marklund]

You have (at least) two easy options.

1) Install old_dssp that is available through the dssp web page.  
2) Install a newer version of gromacs than you have at the moment. What version do you currently use?

Erik

On 12 Jun 2013, at 12:56, Nikunj Maheshwari <nixcrazyforher at gmail.com> wrote:

> Yes I checked. do_dssp has no -ver option.
> I also found out this link
> 
> https://gerrit.gromacs.org/#/c/687/
> 
> but dont know how to install/use it.
> 
> Or maybe I can install DsspOld and see?
> 
> 
> 
> On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> 
>> Search again. The syntax for invoking dssp changed at some point and it
>> took a while before do_dssp adapted to that. If your do_dssp is lacking the
>> -ver option then I'm quite confident that it uses the old syntax, which
>> doesn't work with the newer versions (v. 2.0+ I think) of dssp.
>> 
>> Erik
>> 
>> On 12 Jun 2013, at 11:17, Nikunj Maheshwari <nixcrazyforher at gmail.com>
>> wrote:
>> 
>>> Yes I did searched. But for most people, there were issues regarding the
>>> path or wrong DSSP.
>>> DSSP runs for me, but do_dssp does not.
>>> 
>>> 
>>> On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund <erikm at xray.bmc.uu.se>
>> wrote:
>>> 
>>>> Hi,
>>>> 
>>>> Search the mailing list. This problem and its solution has been
>> repeatedly
>>>> discussed.
>>>> 
>>>> Erik
>>>> 
>>>> On 12 Jun 2013, at 10:31, Nikunj Maheshwari <nixcrazyforher at gmail.com>
>>>> wrote:
>>>> 
>>>>> Dear all,
>>>>> 
>>>>> I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
>>>>> I am trying to use it for do_dssp command but get the following error
>>>> each
>>>>> time:
>>>>> 
>>>>> "Fatal error:
>>>>> Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 >
>>>>> /dev/null 2> /dev/null
>>>>> "
>>>>> 
>>>>> Is there any way to rectify it?
>>>>> 
>>>>> Thanks.
>>>>> Nikunj
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