[gmx-users] Coordinates in hdel.top and hdel.gro not matching

[Alaguraj Veluchamy]

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


ALAGURAJ VELUCHAMY
c/o Dr.S.KRISHNASWAMY,
CENTRE OF  EXCELLENCE IN BIOINFORMATICS,
MADURAI KAMARAJ UNIVERSITY,
MADURAI, TN.
Ph:09486148690
 
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