[gmx-users] Re: IN4 molecule type error

Mark Abraham Mark.Abraham at anu.edu.au
Tue Feb 3 04:33:59 CET 2009

Justin A. Lemkul wrote:
> Ms. Aswathy S wrote:
>> Hi,
>> I have added the #include "drg.itp" statement under the title, ; 
>> Include forcefield parameters in the .top file. Thr drg.itp is saved 
>> in the current directory.
> This is the incorrect order.  You've inserted the drg.itp moleculetype 
> information before your protein, then called the protein before IN4 in 
> the [ molecules ] section.  Order is important.  Include the 
> moleculetypes in the order that they appear in the structure file (.pdb 
> or .gro).

Order is important *within the [molecules] directive*. This order must 
match the intended coordinate file. I don't believe order of the 
[moleculetype] directives is pertinent; chapter 5 doesn't say it is, and 
if it were, the names would be redundant. One could test this by 
juggling the order of water #include directives in some topology. The 
first system that came to hand proved this to be true.

>> Still showing the sanme error as previous.
>> including a part of the top file.Please check this.
>> ________________________________________
>> ;    This is your topology file
>> ;    TRYPSIN
>> ;
>> ; Include forcefield parameters
>> #include "ffgmx.itp"
>> #include "drg.itp"Â
> I don't know if this is just strange behavior from my email client, but 
> if you've got these hidden characters within this line of text, it will 
> not be interpreted correctly.  Make sure you are using a plain text 
> editor, like vi or emacs, to edit your topology file.

Hear, hear.


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