On 4/27/13 12:28 PM, Justin Lemkul wrote:
On 4/27/13 11:21 AM, Nathan Bullock wrote:
I am running genion neutralize the charge of my protein.
I got an error that wasn't very descriptive
Fatal error:
Cannot read from input
The part of the script that called this program read as follows
/usr/local/gromacs-4.5.5/bin/grompp -f em.mdp -c filled_box.pdb -p
protein_mod_filled5.top -o ions.tpr
Was ions.tpr successfully generated?
/usr/local/gromacs-4.5.5/bin/genion -s ions.tpr -o solv_ions.pdb -p
protein_mod_filled5.top -pname NA -nname CL -nn 3
I am using the amber03 force field.
I had read on some of the pages that different forcefields used different
nomenclature for the ions used to neutralize the charge.
This is no longer true as of Gromacs 4.5, which has standardized nomenclature.
You can always check ions.itp for your force field to be sure.
The "cannot read from input error" only arises if (1) you are specifying a
nonexistent index group (not applicable here) or (2) presumably if some input
file does not exist.
Edit: the reason your script fails is that genion requires you to select a group
for replacement. You don't provide one, so it doesn't know what to read. See
the following:
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
-Justin
--
========================================
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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