On 9/24/18 4:58 PM, BIJENDRA KHADKA wrote:
Dear Justin,
As per your suggestion on my previous email, I tried using the ligand (NAD)
input files generated using CHARMM-GUI (files are attached herewith).
The mailing list does not accept attachments.
However, I received the following error.
(previous email:Message-ID: <d3e21a78-9b0c-88fa-a6d7-c60c56a0e...@vt.edu>)
Any suggestion regarding this matter would be greatly appreciated.
command: ./gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
Generally speaking, don't run GROMACS within the directory where it is
installed. It is all too easy to mess something up.
ERROR:
ARNING 15 [file nad.prm, line 21]:
Too few parameters on line (source file
/usr/local/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 943)
None of these errors should be possible if you have sensible files from
CHARMM-GUI. I suspect based on your file names that you're modifying
these files in some way, as you should not need to add ions. Whatever
your modifications are clearly are not correct.
-------------------------------------------------------
Program gmx grompp, VERSION 5.1.4
Source code file:
/usr/local/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c, line: 605
Fatal error:
number of coordinates in coordinate file (solv.gro, 46287)
does not match topology (topol.top, 46288)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
As above, this error is not possible if you simply use the CHARMM-GUI
files. Build the system there, do not modify anything, and proceed with
energy minimization. When you have that done, study the files CHARMM-GUI
has given you to learn about how to properly construct such a system.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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