[gmx-users] Simulating conjugated protein

[Justin Lemkul]

On 5/25/16 12:55 AM, Sanket Ghawali wrote:
> Dear, gmx-users,
>
> Hello everyone,
>
> I'm simulating a peptide in an SDS micelle, where my peptide is conjugated
> to a organic compound at the N terminal. The SDS micelle was genrated using
> CHARMM-GUI, here I am stuck with a problem for adding atom types for the
> compound. I tried adding atomtypes for the compound into the .rtp files of
> the CHARMM forcefield but when i try to run pdb2gmx it throws an error
> regarding missing residues in .hdb file.
>
> I edited the .hdb file adding the hydrogen atom information for the unknown
> compound. The pdb2gmx worked this time but it throws back an error while
> adding ions.
>
> I tried using SwissParam to parameterized the unknown molecule, using this
> i find that the compound does not remain bound to the peptide at the N
> terminal even after merging the compound and peptide co ordinates.
>
> The errors which i get while adding ions:
>
> ERROR 190 [file topol.top, line 3284]:
>   No default Proper Dih. types
>
>
> ERROR 191 [file topol.top, line 3285]:
>   No default Proper Dih. types
>
>
> ERROR 192 [file topol.top, line 3286]:
>   No default Proper Dih. types
>
> Excluding 3 bonded neighbours molecule type 'Protein'
> Excluding 3 bonded neighbours molecule type 'SDS'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 1 bonded neighbours molecule type 'NA'
>
> NOTE 1 [file topol.top, line 3377]:
>   System has non-zero total charge: 17.180007
>   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.
>
>
>
>
> -------------------------------------------------------
> Program grompp, VERSION 4.6.5
> Source code file: /root/Downloads/gromacs-4.6.5/src/kernel/grompp.c, line: 563
>
> Fatal error:
> number of coordinates in coordinate file (sol.gro, 15465)
>              does not match topology (topol.top, 15450)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "Being Great is Not So Good" (Red Hot Chili Peppers)
>
> .
>
>
> Any suggestions on how to go about doing this?
>

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue

You need to properly parametrize the residue in question first, including the 
whole linkage.  Based on the missing parameters and the suspicious charge, your 
underlying parametrization is not functional.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================