[gmx-users] Error in itp file

[Souvik Dey]

You can use this link for ACPYPE:

http://webapps.ccpn.ac.uk/acpype/

First, you have to mail the author and then he would give you a user ID and
password.

On Fri, Aug 4, 2017 at 1:48 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>



-- 
Souvik Dey
Integrated Science Education & Research Centre
Visva Bharati University
Santiniketan-731235
West Bengal
8981736643