[gmx-users] Error while using the CHARMM forcefield for NAD ligand in Gromacs-3

[Justin Lemkul]

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-c60c56a0e488 at 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

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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