[gmx-users] grompp errors

[David van der Spoel]

On 7/13/10 6:11 PM, Amanda Watkins wrote:
> Tue, July 13, 2010 11:46:58 AM
> grompp errors
> ...
> From:	
> Amanda Watkins <mhstrumpetgirl at yahoo.com> [Chat now]
> ...
> View Contact
> To:	gmx-users at gromacs.org	
>
> ------------------------------------------------------------------------
> Dear GROMACS users,
>
> I am trying to simulate a protein (OmpA) and a detergent (DPC) together
> in GROMACS. I have successfully generate and minimized the protein and
> the detergent separately and now I have inserted 216 DPC molecules into
> the protein box, and whenever I try to upload them with grompp for
> mdrun, I get this message:

Not really an answer to your question, but are you aware that this has 
been done already?

- Bond, P. J.; Cuthbertson, J. M.; Deol, S. S.; Sansom, M. S. P. J. Am. 
Chem.
Soc. 2004, 126, 15948.

  - Friemann, Rosmarie; Larsson, Daniel; Wang, Yaofeng; Van der Spoel, 
David: Molecular Dynamics Simulations of a Membrane Protein-Micelle 
Complex in vacuo J. Amer. Chem. Soc. 131 pp. 16606-16607 (2009)
>
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'cpp'
> Replacing old mdp entry 'unconstrained_start' by 'continuation'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18#
> checking input for internal consistency...
>
> NOTE 1 [file em.mdp, line unknown]:
> For energy conservation with switch/shift potentials, rlist should be 0.1
> to 0.3 nm larger than rcoulomb.
>
>
> NOTE 2 [file em.mdp, line unknown]:
> For energy conservation with switch/shift potentials, rlist should be 0.1
> to 0.3 nm larger than rvdw.
>
> processing topology...
> Opening library file /usr/share/gromacs/top/ffG53a6.itp
> Opening library file /usr/share/gromacs/top/ffG53a6nb.itp
> Opening library file /usr/share/gromacs/top/ffG53a6bon.itp
> Opening library file /usr/share/gromacs/top/ff_dum.itp
> Generated 165 of the 1596 non-bonded parameter combinations
> Opening library file /usr/share/gromacs/top/spc.itp
> Opening library file /usr/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 3 bonded neighbours molecule type 'DPC'
>
> NOTE 3 [file 1qjp.top, line 8723]:
> System has non-zero total charge: -1.000001e+00
>
>
>
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
>
> ERROR 1 [file 1qjp.top, line 8723]:
> atom NC3 (Res DPC-1) has mass 0
>
>
>
> ERROR 2 [file 1qjp.top, line 8723]:
> atom PO4 (Res DPC-1) has mass 0
>
>
>
> ERROR 3 [file 1qjp.top, line 8723]:
> atom C1 (Res DPC-1) has mass 0
>
>
>
> ERROR 4 [file 1qjp.top, line 8723]:
> atom C2 (Res DPC-1) has mass 0
>
>
>
> ERROR 5 [file 1qjp.top, line 8723]:
> atom C3 (Res DPC-1) has mass 0
>
>
>
> There were 3 notes
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: ../../../../src/kernel/grompp.c, line: 986
>
> Fatal error:
> There were 5 errors in input file(s)
> -------------------------------------------------------
>
> "Take Your Medications and Preparations and Ram It Up Your Snout" (F. Zappa)
>
>
> *Here is the file that it is having trouble processing:
>
> dpc1.itp:
>
> ; topology for a dodecylphosphocholine lipid
>
> [ moleculetype ]
> ; Name nrexcl
> DPC 3
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 NL 1 DPC NC3 1 0.0 ; qtot: 2.24
> 2 P 1 DPC PO4 1 0.0 ; qtot: 3.28
> 3 CH2 1 DPC C1 1 0.0 ; qtot: 1
> 4 CH2 1 DPC C2 1 0.0 ; qtot: 1
> 5 CH3 1 DPC C3 1 0.0 ; qtot: 3
>
> Is there something that I am inputing wrong? Or is it that I need to
> regenerate the DPC molecules to include all of the atoms within the
> molecule? Whenever I tried to use the other .itp file it gives me the
> error that there is an atom difference. This new error is my attempt to
> fix this error.
>
> Sincerely,
>
> ~Amanda Watkins
>
> SBC 2012
>
>


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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