[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 93

[Sanket Ghawali]

>
>
> Date: Wed, 25 May 2016 07:11:25 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Simulating conjugated protein
> Message-ID: <e0dc7a46-bfcd-ebb0-c188-dd993682a0d8 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> 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
>
> ==================================================
> Thank you Justin for ur reply
>
> I am using Swissparam and Cgenff but the only work for small molecules. I
> was able to generate it for the compound but my peptide is covalently
> linked to the compound at the N terminal so how do i parametrize the whole
> linkage or the whole compound.
> And what name should be given to the compound in the residuetype.dat file.
> Following the SwissParam tutorial:
> http://www.swissparam.ch/
> i was able to work it out upto energy minimization step, I saved the
> initial coordinate of the peptide from the .gro file into .pdb file using
> VMD, when i visualize the .pdb file Discovery studio the compound is not
> bound at the N terminal.
> The tutorial i am using is it correct ?
> Guide me if i am going wrong somewhere.
>

    Thank you.