[gmx-users] Problem executing do_dssp in gromacs

[Justin Lemkul]

On 2/16/15 2:27 AM, Aarti rana wrote:
> Hi Justin,
>
> Yes, I have checked the env variables and file is also executable. But
> still giving fatal error and asking me to specify the dssp version.
>

The error message is just generic, because most times the issue is an incorrect 
version.  You're sure your DSSP binary is 2.0.4?  What does 'echo $DSSP' return?

-Justin

> Aarti
>
>
>
> On Fri, Feb 13, 2015 at 8:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/13/15 4:41 AM, Aarti rana wrote:
>>
>>> Hi,
>>>
>>> I am new to gromacs and using gromacs 4.6.5 and dssp-2.0.4. To study the
>>> secondary structure, when I am running these commands:
>>>
>>> export DSSP=/usr/local/bin/dssp do_dssp -s md_0_1.tpr -f md_0_1_noPBC.xtc
>>> -o dssp.xvg -ver 2
>>>
>>> I am getting this error:
>>>
>>> dssp cmd='/usr/local/bin/dssp -na dd31ZWbc ddI6at3a > /dev/null 2>
>>> /dev/null' Reading frame 0 time 0.000 Back Off! I just backed up dd31ZWbc
>>> to ./#dd31ZWbc.1#
>>>
>>> -------------------------------------------------------Program do_dssp,
>>> VERSION 4.6.5 Source code file:
>>> /build/buildd/gromacs-4.6.5/src/tools/gmx_do_dssp.c, line: 669
>>>
>>> Fatal error: Failed to execute command: Try specifying your dssp version
>>> with the -ver option.
>>>
>>> I have already checked many helping sites but couldn't solve it. I have
>>> also checked the earlier comments posted here.
>>>
>>> I don't know how to fix it. Please help me?
>>>
>>>
>> Is your DSSP environment variable the correct location of the dssp binary
>> and is the dssp binary executable?
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================