[gmx-users] Coordinate file does not match topology

[Sheyore Omovie]

You're right, the total charge is zero. While creating *.top, pdb2gmx did 
not recognise some hydrogen atoms in my pdb file (HA atom type in 
particular).
I had to use -ignh to ignore the H-atoms.
Can I just add this atoms to the *.top like u've stated below, or do I need 
to edit *.rtp to include this particular H-atom.
Rgds
John


>From: Yang Ye <leafyoung at yahoo.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Coordinate file does not match topology
>Date: Sun, 10 Jun 2007 20:00:47 +0800
>
>There is 2312-2291=21 more atoms in your structure file than in the 
>topology file. If it is due to genion, it shall be less. There might be 
>other mistakes in previous steps.
>
>Anyway, to make them match, just count how many molecules you have in the 
>system. The last section in your top file shall be something like
>
>[ molecules ]
>Protein X
>SOL     X
>K+      X
>
>Match the number there. Commands like
>
>grep SOL ABC.gro | wc
>or
>grep Mg ABC.gro | wc
>or
>grep POT ABC.gro | wc
>
>shall be your good companion.
>
>Regards,
>Yang Ye
>
>On 6/10/2007 8:42 AM, Sheyore Omovie wrote:
>>Thanks,
>>But this is my first real simulation, So I'll appreciate it if you can 
>>tell me how to determine the number of ions to add with genion.
>>Thanks
>>John
>>
>>
>>>From: Alan Dodd <anoddlad at yahoo.com>
>>>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>Subject: Re: [gmx-users] Coordinate file does not match topology
>>>Date: Thu, 7 Jun 2007 23:26:01 -0700 (PDT)
>>>
>>>Small errors like that are usually down to things like running genion and 
>>>not changing the .top.  I think I made a problem for myself once with 
>>>non-consecutive atom numbering, too.
>>>
>>>----- Original Message ----
>>>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>>>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>Sent: Friday, June 8, 2007 3:48:28 AM
>>>Subject: Re: [gmx-users] Coordinate file does not match topology
>>>
>>>
>>>Sheyore Omovie wrote:
>>> > Dear gromacs users,
>>> > While trying to preprocess my files with grompp, i got the ff error
>>> > message:
>>> > "Number of coordinates in coordinate file (b4em.gro, 2312) does not
>>> > match topology (twopolypeptide.top, 2291)"
>>> > How can I fix this?
>>>
>>>Make them match. Assuming you haven't managed a gross mismatch of files,
>>>your [molecules] section of your .top probably isn't right. Chapter five
>>>of the manual is your friend here.
>>>
>>>Mark
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