[gmx-users] Error in itp file

[Justin Lemkul]

On 8/3/17 8:53 AM, Souvik Dey wrote:
> ​Yes, I saw the GROMACS website. But my itp file has [atomtypes] first
> followed by [moleculetypes]. So, I am still not getting what is the error.​
> 

All [atomtypes] (and more generally, any force field parameters) must appear 
before *any* [moleculetype] directives, not just the one to which the parameters 
apply.  So a topology that introduces parameters must be #included before any 
invocation of a [moleculetype].

-Justin

> On Thu, Aug 3, 2017 at 2:52 PM, Souvik Dey <souvik.dey29 at gmail.com> wrote:
> 
>> Yes, using ACPYPE is pretty simple. They have a web server, where you can
>> upload your PDB or MOL2 file, provide the charge and multiplicity and it
>> gives you the output file.
>>
>> On Wed, Aug 2, 2017 at 7:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> On 8/2/17 12:35 PM, Souvik Dey wrote:
>>>
>>>> Hi,
>>>>
>>>> I just generated an itp file from ACPYPE. However, if I try to add ions
>>>> it
>>>> shows the following error:
>>>>
>>>> Fatal error:
>>>> Syntax error - File FAD.itp, line 3
>>>> Last line read:
>>>> '[ atomtypes ]'
>>>> Invalid order for directive atomtypes
>>>>
>>>>
>>>> Can somebody say how do I fix this?
>>>>
>>>>
>>> This exact situation is described here:
>>>
>>> http://www.gromacs.org/Documentation/Errors#Invalid_order_fo
>>> r_directive_xxx
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
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>>
>>
>>
>> --
>> Souvik Dey
>> Integrated Science Education & Research Centre
>> Visva Bharati University
>> Santiniketan-731235
>> West Bengal
>> 8981736643
>>
> 
> 
> 

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================