[gmx-users] Input/output error in GROMACS

[Justin Lemkul]

On 9/20/12 8:00 PM, Elie M wrote:
>
> Dear all,
> I am trying to use editconf to produce a .GRO file from an .XYZ file but I am getting the following error:
> "Program editconf, VERSION 4.0.5Source code file: futil.c, line: 330
> File input/output error:S54NONSOLV.xyz.gro"
> Some of the input file is:46S54 NONSOLVATED POLYMERC     5.337500001    -1.902900000     0.000000000C     5.750000001    -2.617400000     0.000000000S     5.197900001    -3.230500000     0.000000000C     4.444300001    -2.894900000     0.000000000C     4.530500001    -2.074400000     0.000000000C     3.015300000    -2.894900000     0.000000000C     3.729800000    -3.307400000     0.000000000C     3.729800000    -4.132400000     0.000000000C     3.015300000    -4.544900001     0.000000000C     2.300800000    -4.132400000     0.000000000C     2.300800000    -3.307400000     0.000000000.......
> The XYZ format is right. Is it that editconf cannot read .XYZ files although I understood otherwise..

A closer look at the code indicates that .xyz files are only read in certain 
circumstances, but I haven't looked closely.  The fatal error indicates quite 
clearly that .xyz files are not accepted, since editconf appends a .gro 
extension to your file name.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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