Re: [gmx-users] Ligand topology in topol.top

[Steven Neumann]

On Tue, Nov 1, 2011 at 5:44 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>
>>
>> On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Steven Neumann wrote:
>>
>>Hi Guys,
>> I am using Charmm27 ff for my protein and ligand system. I used
>>SwissParam to generate the topology for my ligand. I included
>>the obtained topology of my ligand as in Justin tutorial:
>> ; Include Position restraint file
>>
>>#ifdef POSRES
>>
>>#include "posre.itp"
>>
>>#endif
>>
>>; Include ligand topology
>>
>>#include "ligand.itp"
>>
>>; Ligand position restraints
>>
>>#ifdef POSRES
>>
>>#include "posre_ligand.itp"
>>
>>#endif
>>
>>; Include water topology
>>
>>#include "charmm27.ff/tip3p.itp"
>>
>> When I wanted to run NVT I obtained:
>> Fatal error:
>>Syntax error - File egcg.itp, line 7
>>Last line read:
>>'[ atomtypes ] '
>>Invalid order for directive atomtypes
>> However when I included my topology as:
>> ; Include forcefield parameters
>>
>>#include "charmm27.ff/forcefield.itp"
>>
>>#include "ligand.itp"
>>
>>[ moleculetype ]
>>
>>; Name nrexc
>>
>>..
>>
>>; Include Position restraint file
>>
>>#ifdef POSRES
>>
>>#include "posre.itp"
>>
>>#endif
>>
>>; Ligand position restraints
>>
>>#ifdef POSRES
>>
>>#include "posre_egcg.itp"
>>
>>#endif
>>
>>; Include water topology
>>
>>#include "charmm27.ff/tip3p.itp"
>>
>>
>> Everything seems to be ok!
>>Any clue why is that?
>>
>>
>>The topology must follow a defined order.  Please consult Chapter 5
>>of the manual for the required hierarchy.  Of course, the latter
>>case will also not work, because you've introduced ligand position
>>restraints after the protein [moleculetype], so if invoked, they
>>will cause a different fatal error.
>>
>>The Gromacs site also has more on these types of errors, as well as
>>the list archive, where this error has been posted and solved
>>hundreds of times.
>>
>>-Justin
>>
>>Thank you Justin! But actually the last case I provided actually
>>works...
>>
>>
> Then the position restraints are not being applied to the ligand.  They
> can't be.  Once the protein [moleculetype] is introduced, all
> [position_restraints] directives immediately after are applied to it.  Try
> invoking the restraints separately, i.e. with "define = -DPOSRES
> -DPOSRES_LIGAND" and you will get a fatal error.
>
>
> -Justin
>


You are as always right :) Thanks!

Steven
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Ligand topology in topol.top

[Justin A. Lemkul]

Steven Neumann wrote:



On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul > wrote:




Steven Neumann wrote:

Hi Guys,
 I am using Charmm27 ff for my protein and ligand system. I used
SwissParam to generate the topology for my ligand. I included
the obtained topology of my ligand as in Justin tutorial:
 
; Include Position restraint file


#ifdef POSRES

#include "posre.itp"

#endif

; Include ligand topology

#include "ligand.itp"

; Ligand position restraints

#ifdef POSRES

#include "posre_ligand.itp"

#endif

; Include water topology

#include "charmm27.ff/tip3p.itp"

 When I wanted to run NVT I obtained:
 Fatal error:
Syntax error - File egcg.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
 However when I included my topology as:
 
; Include forcefield parameters


#include "charmm27.ff/forcefield.itp"

#include "ligand.itp"

[ moleculetype ]

; Name nrexc

..

; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

; Ligand position restraints

#ifdef POSRES

#include "posre_egcg.itp"

#endif

; Include water topology

#include "charmm27.ff/tip3p.itp"


 Everything seems to be ok!
Any clue why is that?
 



The topology must follow a defined order.  Please consult Chapter 5
of the manual for the required hierarchy.  Of course, the latter
case will also not work, because you've introduced ligand position
restraints after the protein [moleculetype], so if invoked, they
will cause a different fatal error.

The Gromacs site also has more on these types of errors, as well as
the list archive, where this error has been posted and solved
hundreds of times.

-Justin

Thank you Justin! But actually the last case I provided actually
works...



Then the position restraints are not being applied to the ligand.  They can't 
be.  Once the protein [moleculetype] is introduced, all [position_restraints] 
directives immediately after are applied to it.  Try invoking the restraints 
separately, i.e. with "define = -DPOSRES -DPOSRES_LIGAND" and you will get a 
fatal error.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Ligand topology in topol.top

[Steven Neumann]

On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>> Hi Guys,
>>  I am using Charmm27 ff for my protein and ligand system. I used
>> SwissParam to generate the topology for my ligand. I included the obtained
>> topology of my ligand as in Justin tutorial:
>>
>> ; Include Position restraint file
>>
>> #ifdef POSRES
>>
>> #include "posre.itp"
>>
>> #endif
>>
>> ; Include ligand topology
>>
>> #include "ligand.itp"
>>
>> ; Ligand position restraints
>>
>> #ifdef POSRES
>>
>> #include "posre_ligand.itp"
>>
>> #endif
>>
>> ; Include water topology
>>
>> #include "charmm27.ff/tip3p.itp"
>>
>>  When I wanted to run NVT I obtained:
>>  Fatal error:
>> Syntax error - File egcg.itp, line 7
>> Last line read:
>> '[ atomtypes ] '
>> Invalid order for directive atomtypes
>>  However when I included my topology as:
>>
>> ; Include forcefield parameters
>>
>> #include "charmm27.ff/forcefield.itp"
>>
>> #include "ligand.itp"
>>
>> [ moleculetype ]
>>
>> ; Name nrexc
>>
>> ..
>>
>> ; Include Position restraint file
>>
>> #ifdef POSRES
>>
>> #include "posre.itp"
>>
>> #endif
>>
>> ; Ligand position restraints
>>
>> #ifdef POSRES
>>
>> #include "posre_egcg.itp"
>>
>> #endif
>>
>> ; Include water topology
>>
>> #include "charmm27.ff/tip3p.itp"
>>
>> 
>>  Everything seems to be ok!
>> Any clue why is that?
>>
>>
>
> The topology must follow a defined order.  Please consult Chapter 5 of the
> manual for the required hierarchy.  Of course, the latter case will also
> not work, because you've introduced ligand position restraints after the
> protein [moleculetype], so if invoked, they will cause a different fatal
> error.
>
> The Gromacs site also has more on these types of errors, as well as the
> list archive, where this error has been posted and solved hundreds of times.
>
> -Justin
>
> Thank you Justin! But actually the last case I provided actually works...


Steven
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Ligand topology in topol.top

[Justin A. Lemkul]

Steven Neumann wrote:

Hi Guys,
 
I am using Charmm27 ff for my protein and ligand system. I used 
SwissParam to generate the topology for my ligand. I included the 
obtained topology of my ligand as in Justin tutorial:
 


; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

; Include ligand topology

#include "ligand.itp"

; Ligand position restraints

#ifdef POSRES

#include "posre_ligand.itp"

#endif

; Include water topology

#include "charmm27.ff/tip3p.itp"

 
When I wanted to run NVT I obtained:
 
Fatal error:

Syntax error - File egcg.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
 
 
However when I included my topology as:
 


; Include forcefield parameters

#include "charmm27.ff/forcefield.itp"

#include "ligand.itp"

[ moleculetype ]

; Name nrexc

..

; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

; Ligand position restraints

#ifdef POSRES

#include "posre_egcg.itp"

#endif

; Include water topology

#include "charmm27.ff/tip3p.itp"


 
Everything seems to be ok!

Any clue why is that?
 


The topology must follow a defined order.  Please consult Chapter 5 of the 
manual for the required hierarchy.  Of course, the latter case will also not 
work, because you've introduced ligand position restraints after the protein 
[moleculetype], so if invoked, they will cause a different fatal error.


The Gromacs site also has more on these types of errors, as well as the list 
archive, where this error has been posted and solved hundreds of times.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists