[gmx-users] grompp errors

[Justin A. Lemkul]

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:
> 
> 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 

Do you have incomplete molecules?  That would seem to be a huge problem.

The errors come from the fact that you do not have masses listed in the topology 
for at least a few of your atoms.  See Chapter 5 for the topology format, but 
more importantly, note that you have a "mass" column with nothing under it.

-Justin

> error that there is an atom difference. This new error is my attempt to 
> fix this error.
> 
> Sincerely,
> 
> ~Amanda Watkins
> 
> SBC 2012
> 
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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