2 jun 2007 kl. 08.59 skrev David van der Spoel:
Alaguraj Veluchamy wrote:
Dear gmx-users,
I am trying to simulate protein-DNA complex and i am using AMBER
port for ForceField. I have edited my PDB and spc.itp to suit
parameters. While preprocessing the following error is shown.
The number of atoms in .top and .gro files are not matching. It is
not taking into account the number of solvent molecule (74040)
which are added during the genbox. I tried summing up water (391)
in PDB and solvating water (74040) in a single line in hdel.top.
Then it shows error difference in atom (391+74040).
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11#
checking input for internal consistency...
calling /lib/cpp -traditional...
Tried to execute: '/lib/cpp -traditional -I/usr/local/gromacs/
share/top -D_FF_A
MBER2 hdel.top > grompp1LWQAw'
The '/lib/cpp -traditional' command is defined in the .mdp file
processing topology...
Generated 2628 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2628 of the 2628 1-4 parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
Excluding 3 bonded neighbours for Protein_B 1
Excluding 3 bonded neighbours for Protein_5 1
Excluding 3 bonded neighbours for Protein_C 1
Excluding 3 bonded neighbours for Protein_3 1
Excluding 3 bonded neighbours for Protein_D 1
Excluding 2 bonded neighbours for SOL 391
Excluding 2 bonded neighbours for SOL 74040
WARNING 1 [file "hdel.top", line 47]:
System has non-zero total charge: -1.502655e+02
processing coordinates...
Fatal error: number of coordinates in coordinate file (hdel.gro,
302737)
does not match topology (hdel.top, 228697)
Is this error due to charge ? In this case i am unable to use
genion as it needs .tpr generated by grompp. how the coordinates
are not matching. Is last line of .top file is not read.
Thanks and regards
could it be that you have tip4p in the gro file and selected tip3p
or spc in pdb2gmx? The charge should be integer, so check the
spc.itp file that you have edited.
The non-integer-charge-problem is associated with the amber port
itself. There are three easy workarounds documented on the amber port
homepage.
/Erik
--
David.
______________________________________________________________________
__
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
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