[gmx-users] Fatal error:Library file aminoacids.dat not found in current dir nor in default directories

[Jinyao Wang]

Hi,gmx-users
I am running a editconf commond like this,
editconf_d -f *.gro -bt cubic -c -d 2.5 -o box.gro
but I am getting the following the fatal error:
Fatal error:
Library file aminoacids.dat not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)
How can I solve it?
Thank you in advance



Jinyao Wang Ph.D. Candidate
State Key Laboratory of Electroanalytical Chemistry
ChangChun Institute of Applied Chemistry (CIAC)
Chinese Academy of Sciences (CAS)
Address: 5625 Renmin Street, Changchun 130022, P.R. China
Tel.: [phone]
Email: wangjy at ciacjl.cn

URL: http://fyzhao.ciac.jl.cn
http://www.ciac.jl.cn
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[Mark Abraham]

Post by Jinyao Wang
Hi,gmx-users
I am running a editconf commond like this,
editconf_d -f *.gro -bt cubic -c -d 2.5 -o box.gro
Library file aminoacids.dat not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)
How can I solve it?

See
http://wiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation

Mark

[Oliver Stueker]

Post by Mark Abraham

Post by Jinyao Wang
Hi,gmx-users
I am running a editconf commond like this,
editconf_d -f *.gro -bt cubic -c -d 2.5 -o box.gro
Library file aminoacids.dat not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)
How can I solve it?

See
http://wiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation
Mark

The procedure on that Wiki-Page actually works in (from my personal experience)
only ~90% of the cases:

After I installed Gromacs 4.0.5 on a Cluster in my home-directory, tools like
pdb2gmx kept complaining they couldn't find the topology files, as GMXLIB was
actually not set by GMXRC.

Fortunately adding the line:
export GMXLIB="${GMXDATA}/gromacs/top"

just after sourcing GMXRC in my .bashrc, worked for me.

Oliver

[Mark Abraham]

Post by Oliver Stueker

Post by Mark Abraham

Post by Jinyao Wang
Hi,gmx-users
I am running a editconf commond like this,
editconf_d -f *.gro -bt cubic -c -d 2.5 -o box.gro
Library file aminoacids.dat not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)
How can I solve it?

See
http://wiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation
Mark

The procedure on that Wiki-Page actually works in (from my personal experience)
After I installed Gromacs 4.0.5 on a Cluster in my home-directory, tools like
pdb2gmx kept complaining they couldn't find the topology files, as GMXLIB was
actually not set by GMXRC.
export GMXLIB="${GMXDATA}/gromacs/top"
just after sourcing GMXRC in my .bashrc, worked for me.

Sigh, indeed, you're right. I've always "overridden" GMXLIB by hand to
accommodate some of my foibles. GMXRC not setting GMXLIB seems to defeat
the point.

Mark