[gmx-users] Coordinate file does not match topology

[Sheyore Omovie]

Thanks Yang,
Each of the residues in my *.gro have more H-atoms than in *.top. I added 
the 21 H-atoms in [molecules] section of *.top. But grompp still came up 
with the ff error: No such molecule type.
Do i have to edit [moleculetype] section too?
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 23:02:29 +0800
>
>
>
>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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