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

[Justin Lemkul]

On 9/17/18 11:11 AM, BIJENDRA KHADKA wrote:
> Hello Everyone,
> Recieved an following error while using the CHARMM forcefield for
> NAD-protein interaction.
> All suitable gromacs topology files for ligand was generated using the the
> python script (and procedure) described in the MacKerell website.

You generated a CGenFF version of NAD? You don't need to do this, 
NAD(P)(H) are all already built into CHARMM36. The error you're getting 
probably stems from "new" CGenFF parameters you've forgotten to #include 
in your topology.

But again, you shouldn't be doing this. Just process the structure with 
pdb2gmx (provided all the atoms are named correctly) or build the system 
with the CHARMM-GUI server.

-Justin

> The nad.itp file is attached herewith
>
> Any suggestions would be greatly appreciated.
>
>
> Step: Addition of ion.
> Follwining is the error output:
>
> NOTE 1 [file ions.mdp]:
>    With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>    that with the Verlet scheme, nstlist has no effect on the accuracy of
>    your simulation.
>
> Setting the LD random seed to 3260613728
> Generated 97877 of the 97903 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 64492 of the 97903 1-4 parameter combinations
> ERROR 1 [file nad.itp, line 91]:
>    No default Bond types
> ERROR 2 [file nad.itp, line 104]:
>    No default Bond types
> ERROR 3 [file nad.itp, line 350]:
>    No default U-B types
> ERROR 4 [file nad.itp, line 352]:
>    No default U-B types
> ERROR 5 [file nad.itp, line 354]:
>    No default U-B types
> ERROR 6 [file nad.itp, line 450]:
>    No default U-B types
> ERROR 7 [file nad.itp, line 458]:
>    No default U-B types
> ERROR 8 [file nad.itp, line 459]:
>    No default U-B types
> ERROR 9 [file nad.itp, line 485]:
>    No default Proper Dih. types
> ERROR 10 [file nad.itp, line 486]:
>    No default Proper Dih. types
> ERROR 11 [file nad.itp, line 487]:
>    No default Proper Dih. types
> ERROR 12 [file nad.itp, line 489]:
>    No default Proper Dih. types
> ERROR 13 [file nad.itp, line 653]:
>    No default Proper Dih. types
> ERROR 14 [file nad.itp, line 654]:
>    No default Proper Dih. types
> ERROR 15 [file nad.itp, line 655]:
>    No default Proper Dih. types
> Excluding 3 bonded neighbours molecule type 'Protein_chain_R'
> turning H bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'NAD'
> turning H bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning H bonds into constraints...
>
> NOTE 2 [file topol.top, line 44763]:
>    System has non-zero total charge: -10.999996
>    Total charge should normally be an integer. See
>    http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>    for discussion on how close it should be to an integer.
>
>
> Regards,
> Bijen
> --
>
>

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

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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