[gmx-users] problem with pdb2gmx

[Justin Lemkul]

On 5/1/14, 6:02 AM, Nizar Masbukhin wrote:
> Hi, friends. I’m new to gromacs. I’m trying to learn it based on  tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html.
> Whenever i input pdb2gmx line, i always get this message:
>
> Using the Oplsaa force field in directory oplsaa.ff
>
> Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
> Reading 1AKI.pdb...
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.5
> Source code file: futil.c, line: 491
>
> File input/output error:
> 1AKI.pdb
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> What is wrong? can anyone explain? and what is the solution?
>

The error means that 1AKI.pdb is not in your working directory.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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