[gmx-users] Coordinate file does not match topology

[Yang Ye]

On 6/10/2007 8:54 PM, Sheyore Omovie wrote:
> 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.
No. This is not the reason why there are different number of atoms 
inside your .gro and .top. pdb2gmx shall always generate a correct top.
> 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.
Check other steps. Or check what's the difference (which type of 
molecule has more number) if you want to find the root of the problem? 
Or just proceed with my suggested modification.
> 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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