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

[Erik Marklund]

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
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> ++++
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the www  
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_______________________________________________
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
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys