[gmx-users] making a box of water

[Payman Pirzadeh]

Will #include "ffgmx.itp" solve my problem? Would it be a general solution
or in each case I should specify (if I add other solutes such as proteins)?

Payman

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 14, 2009 7:07 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water


You need to #include an appropriate force field that contains the
[defaults], 
[atomtypes], etc. before you can define a [moleculetype].

-Justin

Payman Pirzadeh wrote:
> Here is my .top file:
> 
> ;This includes SPC-E potential
> #include "spce.itp"
> 
> [ system ]
> Pure box of water
> 
> [ molecules ]
> SOL             515
> 
> I used the same thing with my own model, but it had worked.
> 
> Payman
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Justin A. Lemkul
> Sent: July 14, 2009 6:54 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] making a box of water
> 
> 
> 
> Payman Pirzadeh wrote:
>> Hello,
>>
>> I am trying to make a box of water from three different water models. I 
>> can make one from my own water model, but when I want to test TIP4P and 
>> SPCE, as soon as it comes to energy minimization step and using grompp, 
>> I get the following error message:
>>
>>  
>>
>> Program grompp, VERSION 4.0.4
>>
>> Source code file: topio.c, line: 415
>>
>>  
>>
>> Fatal error:
>>
>> Syntax error - File spce.itp, line 1
>>
>> Last line read:
>>
>> '[ moleculetype ]'
>>
>> Invalid order for directive moleculetype
>>
>>  
>>
>> What is the problem causing the code referring to itp file?
>>
> 
> See the message I just sent.  Something is out of order in your .top file.
> 
> -Justin
> 
>> Regards,
>>
>>  
>>
>> Payman
>>
>>  
>>
>>
>> ------------------------------------------------------------------------
>>
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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