On 7/13/10 6:11 PM, Amanda Watkins wrote:
Tue, July 13, 2010 11:46:58 AM
grompp errors
...
From:
Amanda Watkins <[email protected]> [Chat now]
...
View Contact
To: [email protected]
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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
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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
[email protected] [email protected] http://folding.bmc.uu.se
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