[gmx-users] Problem executing do_dssp in gromacs
ranaaarti.hp at gmail.com
Mon Feb 16 08:27:31 CET 2015
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.
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:
>> 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 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
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