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 <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@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 <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@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 <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <gmx-users@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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