Re: [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  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  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  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

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

 ==

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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
>
> jalem...@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
> /Mailing_Lists/GMX-Users_List before posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>



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

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

==

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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

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

==
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Re: [gmx-users] Error in itp file

[Mohammad Zahidul Hossain Khan]

write the ligand topology just after the forcefield parameter.

; Include forcefield parameters
#include "amber03.ff/forcefield.itp"

; Include ligand topology
#include "drg.itp"

On Thu, Aug 3, 2017 at 5:53 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.​
>
> On Thu, Aug 3, 2017 at 2:52 PM, Souvik Dey  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  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
> >>
> >> jalem...@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
> >> /Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
> >
> > --
> > Souvik Dey
> > Integrated Science Education & Research Centre
> > Visva Bharati University
> > Santiniketan-731235
> > West Bengal
> > 8981736643
> >
>
>
>
> --
> Souvik Dey
> Integrated Science Education & Research Centre
> Visva Bharati University
> Santiniketan-731235
> West Bengal
> 8981736643
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.




-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
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Re: [gmx-users] Error in itp file

[Mohammad Zahidul Hossain Khan]

Can you give web server link? I have tried but didn't find.

On Aug 3, 2017 5:53 AM, "Souvik Dey"  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  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_
> > for_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
> >
> > jalem...@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
> > /Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Souvik Dey
> Integrated Science Education & Research Centre
> Visva Bharati University
> Santiniketan-731235
> West Bengal
> 8981736643
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Error in itp file

[Souvik Dey]

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  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_
> for_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
>
> jalem...@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
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



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

* Please search the archive at 
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Re: [gmx-users] Error in itp file

[Justin Lemkul]

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_for_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

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

==
--
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Re: [gmx-users] Error in itp file

[Mohammad Zahidul Hossain Khan]

Hi

Can you tell me, how have you used ACPYPE for itp.

On Aug 2, 2017 9:36 AM, "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?
>
> Regards,
> Souvik Dey
>
> --
> Souvik Dey
> Integrated Science Education & Research Centre
> Visva Bharati University
> Santiniketan-731235
> West Bengal
> 8981736643
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Error in itp file

[Souvik Dey]

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?

Regards,
Souvik Dey

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

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