Thanks guys,
I've finally resolved it.
I think gromacs has an issue with the naming convention used in the pdb file
I created with pymol.
So I started all over again, stripped the pdb file of its H-atoms. That way,
both pdb2gmx and grompp worked just fine. pdb2gmx added the H-atoms I need
in the structure.
Rgds
John
From: Yang Ye <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Subject: Re: [gmx-users] Coordinate file does not match topology
Date: Mon, 11 Jun 2007 10:17:49 +0800
On 6/11/2007 4:27 AM, David van der Spoel wrote:
Sheyore Omovie wrote:
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
Please do not edit the topology file unless you are very sure what you are
doing. You probably select a united atom force field and want to combine
it with an all atom coordinate file. You will have to use the conf.gro
that pdb2gmx produces.
Hi, Omovie
Hope David's comment help you to understand what you are doing with the
step of grompp. No individual H-atom shall exist outside a molecule as we
are not doing nuclear simulation. =)
Regards,
Yang Ye
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