[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=20
> did not recognise some hydrogen atoms in my pdb file (HA atom type in=20
> particular).
> I had to use -ignh to ignore the H-atoms.
No. This is not the reason why there are different number of atoms=20
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=20
> need to edit *.rtp to include this particular H-atom.
Check other steps. Or check what's the difference (which type of=20
molecule has more number) if you want to find the root of the problem?=20
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=3D21 more atoms in your structure file than in the=20
>> topology file. If it is due to genion, it shall be less. There might=20
>> be other mistakes in previous steps.
>>
>> Anyway, to make them match, just count how many molecules you have in=20
>> 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=20
>>> 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=20
>>>> genion and not changing the .top.  I think I made a problem for=20
>>>> 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 erro=
r
>>>> > message:
>>>> > "Number of coordinates in coordinate file (b4em.gro, 2312) does no=
t
>>>> > match topology (twopolypeptide.top, 2291)"
>>>> > How can I fix this?
>>>>
>>>> Make them match. Assuming you haven't managed a gross mismatch of=20
>>>> files,
>>>> your [molecules] section of your .top probably isn't right. Chapter=20
>>>> five
>>>> of the manual is your friend here.
>>>>
>>>> Mark
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