Re: [gmx-users] Position Restraints of one of the moleculetpye

2012-05-29 Thread Steven Neumann 
On Tue, May 29, 2012 at 12:21 PM, Justin A. Lemkul  wrote:

>
>
> On 5/29/12 6:52 AM, Steven Neumann wrote:
>
>> Ok. My topology:
>>
>> ; Include forcefield parameters
>> #include "./charmm27.ff/forcefield.itp"
>>
>> ; Include ligand topology
>> #include "ligand1.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_1
>> #include "posre_ligand1.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand2.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_2
>> #include "posre_ligand2.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand3.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_3
>> #include "posre_ligand3.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand4.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_4
>> #include "posre_ligand4.itp"
>> #endif
>>
>>
>> ; Include ligand topology
>> #include "ligand5.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_5
>> #include "posre_ligand5.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand6.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_6
>> #include "posre_ligand6.itp"
>> #endif
>>
>> ; Include water topology
>> #include "./charmm27mod.ff/tip3p.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct   fcxfcyfcz
>>11   1000   1000   1000
>> #endif
>>
>> ; Include topology for ions
>> #include "./charmm27.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> Protein in water
>>
>> [ molecules ]
>> ; Compound#mols
>> ligand1   1
>> ligand2   1
>> ligand3   1
>> ligand4   1
>> ligand5   1
>> ligand6   1
>> SOL  4617
>>
>>
>> Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other
>> information
>> is the same
>>
>> posre_ligand1.itp - ... - posre_ligand2.itp are all the same files.
>>
>> Then when I grompp:
>>
>> Syntax error - File ligand2.itp, line 7
>> Last line read:
>> '[ atomtypes ] '
>> Invalid order for directive atomtypes
>>
>> Any suggestions appreciated,
>>
>>
> Once you declare a [moleculetype], the other force field-level directives
> cannot be called.  If all the ligand topologies are the same, remove
> [atomtypes] from all but the first.
>
>
> -Justin
>

Thanks Justin. Removing [pairtypes] and [atomtypes] from all but not the
first helped.

Steven



> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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/**
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Re: [gmx-users] Position Restraints of one of the moleculetpye

2012-05-29 Thread Justin A. Lemkul 



On 5/29/12 6:52 AM, Steven Neumann wrote:

Ok. My topology:

; Include forcefield parameters
#include "./charmm27.ff/forcefield.itp"

; Include ligand topology
#include "ligand1.itp"

; Include Position restraint file
#ifdef POSRES_1
#include "posre_ligand1.itp"
#endif

; Include ligand topology
#include "ligand2.itp"

; Include Position restraint file
#ifdef POSRES_2
#include "posre_ligand2.itp"
#endif

; Include ligand topology
#include "ligand3.itp"

; Include Position restraint file
#ifdef POSRES_3
#include "posre_ligand3.itp"
#endif

; Include ligand topology
#include "ligand4.itp"

; Include Position restraint file
#ifdef POSRES_4
#include "posre_ligand4.itp"
#endif


; Include ligand topology
#include "ligand5.itp"

; Include Position restraint file
#ifdef POSRES_5
#include "posre_ligand5.itp"
#endif

; Include ligand topology
#include "ligand6.itp"

; Include Position restraint file
#ifdef POSRES_6
#include "posre_ligand6.itp"
#endif

; Include water topology
#include "./charmm27mod.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
#endif

; Include topology for ions
#include "./charmm27.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
ligand1   1
ligand2   1
ligand3   1
ligand4   1
ligand5   1
ligand6   1
SOL  4617


Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other information
is the same

posre_ligand1.itp - ... - posre_ligand2.itp are all the same files.

Then when I grompp:

Syntax error - File ligand2.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes

Any suggestions appreciated,



Once you declare a [moleculetype], the other force field-level directives cannot 
be called.  If all the ligand topologies are the same, remove [atomtypes] from 
all but the first.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Re: [gmx-users] Position Restraints of one of the moleculetpye

2012-05-29 Thread Steven Neumann 
Ok. My topology:

; Include forcefield parameters
#include "./charmm27.ff/forcefield.itp"

; Include ligand topology
#include "ligand1.itp"

; Include Position restraint file
#ifdef POSRES_1
#include "posre_ligand1.itp"
#endif

; Include ligand topology
#include "ligand2.itp"

; Include Position restraint file
#ifdef POSRES_2
#include "posre_ligand2.itp"
#endif

; Include ligand topology
#include "ligand3.itp"

; Include Position restraint file
#ifdef POSRES_3
#include "posre_ligand3.itp"
#endif

; Include ligand topology
#include "ligand4.itp"

; Include Position restraint file
#ifdef POSRES_4
#include "posre_ligand4.itp"
#endif


; Include ligand topology
#include "ligand5.itp"

; Include Position restraint file
#ifdef POSRES_5
#include "posre_ligand5.itp"
#endif

; Include ligand topology
#include "ligand6.itp"

; Include Position restraint file
#ifdef POSRES_6
#include "posre_ligand6.itp"
#endif

; Include water topology
#include "./charmm27mod.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "./charmm27.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
ligand1   1
ligand2   1
ligand3   1
ligand4   1
ligand5   1
ligand6   1
SOL  4617


Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other
information is the same

posre_ligand1.itp - ... - posre_ligand2.itp are all the same files.

Then when I grompp:

Syntax error - File ligand2.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes

Any suggestions appreciated,

Steven




On Mon, May 28, 2012 at 5:25 PM, Justin A. Lemkul  wrote:

>
>
> On 5/28/12 10:48 AM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> I am fighting with the position restraints. My system cosnsists of 6
>> ligands -
>> all of them have the same topology - ligand.itp. I want to:
>>
>> 1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L,
>> posre
>> ligand1.itp
>> 2. Restrain 5 of them and pull one of them away.
>>
>> Here I came across some difficulties.
>>
>> I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp
>>
>> and by index files I create an index of the ligands I wan to restrain.
>> Each my
>> ligands has 46 atoms. When I process to grompp:
>>
>> Atom index (256) in position_restraints out of bounds (1-46).
>> This probably means that you have inserted topology section
>> "position_restraints
>>
>> Shall I rename Ligands as different residue names? If my posre includes
>> 1-46
>> atom all ligands are restraints? How to restrain just 5 out of 6 of them?
>>
>>
> Position restraints are applied on a per-moleculetype basis.  If you have
> six copies of a ligand, the only way to do this is to define the sixth as a
> special [moleculetype] (even if it contains identical information) with a
> different name, such that it can be restrained in the absence of restraints
> on the others.  See the logic here:
>
> http://www.gromacs.org/**Documentation/Errors#Atom_**index_n_in_position_*
> *restraints_out_of_bounds
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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/Searchbefore
>  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
>
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Re: [gmx-users] Position Restraints of one of the moleculetpye

2012-05-28 Thread Justin A. Lemkul 



On 5/28/12 10:48 AM, Steven Neumann wrote:

Dear Gmx Users,

I am fighting with the position restraints. My system cosnsists of 6 ligands -
all of them have the same topology - ligand.itp. I want to:

1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L, posre
ligand1.itp
2. Restrain 5 of them and pull one of them away.

Here I came across some difficulties.

I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp

and by index files I create an index of the ligands I wan to restrain. Each my
ligands has 46 atoms. When I process to grompp:

Atom index (256) in position_restraints out of bounds (1-46).
This probably means that you have inserted topology section "position_restraints

Shall I rename Ligands as different residue names? If my posre includes 1-46
atom all ligands are restraints? How to restrain just 5 out of 6 of them?



Position restraints are applied on a per-moleculetype basis.  If you have six 
copies of a ligand, the only way to do this is to define the sixth as a special 
[moleculetype] (even if it contains identical information) with a different 
name, such that it can be restrained in the absence of restraints on the others. 
 See the logic here:


http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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[gmx-users] Position Restraints of one of the moleculetpye

2012-05-28 Thread Steven Neumann 
Dear Gmx Users,

I am fighting with the position restraints. My system cosnsists of 6
ligands - all of them have the same topology - ligand.itp. I want to:

1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L,
posre ligand1.itp
2. Restrain 5 of them and pull one of them away.

Here I came across some difficulties.

I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp

and by index files I create an index of the ligands I wan to restrain. Each
my ligands has 46 atoms. When I process to grompp:

Atom index (256) in position_restraints out of bounds (1-46).
This probably means that you have inserted topology section
"position_restraints

Shall I rename Ligands as different residue names? If my posre includes
1-46 atom all ligands are restraints? How to restrain just 5 out of 6 of
them?

Best,

Steven
-- 
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