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

[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.


-- 
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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