subject:"\[gmx\-users\] Topology include file \" \" not found"

Re: [gmx-users] Topology include file " " not found

2016-04-26 Thread Mark Abraham

Yeah, don't use wysiwyg word processors for editing plain text files (else
you will get such smartness tripping you up). Use an editor aimed at them.

Mark

On Tue, 26 Apr 2016 13:59 gozde ergin  wrote:

> Ok I found the error. I put “cis-pinonic.itp” instead of
> ”cis-pinonic.itp”. The problem is quote.
>
> On 26 Apr 2016, at 13:35, gozde ergin  wrote:
> >
> > I checked it and there is no #include statement in cis-pinonic.itp file.
> >> On 26 Apr 2016, at 13:24, Justin Lemkul  wrote:
> >>
> >>
> >>
> >> On 4/26/16 5:57 AM, gozde ergin wrote:
> >>> Dear all,
> >>>
> >>> I am trying to simulate organic system.
> >>> Here is my tool.top file, and cis-pionic,its is in the same folder
> with the tool.top.
> >>>
> >>> ;
> >>> ; Topology from .mol2 file
> >>> ; topolbuild
> >>> ;
> >>> ; The force field files to be included
> >>> #include "charmm27.ff/forcefield.itp"
> >>>
> >>> ; Include chain topologies
> >>> #include “cis-pinonic.itp"
> >>>
> >>> ; Include water topology
> >>> #include "charmm27.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 ]
> >>> ; title from mol2 input
> >>> LIG
> >>>
> >>> [ molecules ]
> >>> ; molecule namenr.
> >>> cis-pinonic   64
> >>>
> >>>
> >>> When I try to minimize the system this is the error that I’m getting,
> >>>
> >>> grompp -f minim.mdp  -c lig.gro -p topol.top -o em.tpr
> >>>
> >>> Fatal error:
> >>> Topology include file "   " not found
> >>> For more information and tips for troubleshooting, please check the
> GROMACS
> >>> website at http://www.gromacs.org/Documentation/Errors
> >>>
> >>> What is that mean?
> >>> I thought maybe there is an invisible line so I did also dos2unix
> however the error is still there.
> >>>
> >>
> >> Are there any #include statements within your .itp files (e.g.
> cis-pinonic.itp) that might be triggering this?
> >>
> >> -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.
> >
>
> --
> 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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Re: [gmx-users] Topology include file " " not found

2016-04-26 Thread gozde ergin

Ok I found the error. I put “cis-pinonic.itp” instead of ”cis-pinonic.itp”. The 
problem is quote.

On 26 Apr 2016, at 13:35, gozde ergin  wrote:
> 
> I checked it and there is no #include statement in cis-pinonic.itp file.
>> On 26 Apr 2016, at 13:24, Justin Lemkul  wrote:
>> 
>> 
>> 
>> On 4/26/16 5:57 AM, gozde ergin wrote:
>>> Dear all,
>>> 
>>> I am trying to simulate organic system.
>>> Here is my tool.top file, and cis-pionic,its is in the same folder with the 
>>> tool.top.
>>> 
>>> ;
>>> ; Topology from .mol2 file
>>> ; topolbuild
>>> ;
>>> ; The force field files to be included
>>> #include "charmm27.ff/forcefield.itp"
>>> 
>>> ; Include chain topologies
>>> #include “cis-pinonic.itp"
>>> 
>>> ; Include water topology
>>> #include "charmm27.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 ]
>>> ; title from mol2 input
>>> LIG
>>> 
>>> [ molecules ]
>>> ; molecule namenr.
>>> cis-pinonic   64
>>> 
>>> 
>>> When I try to minimize the system this is the error that I’m getting,
>>> 
>>> grompp -f minim.mdp  -c lig.gro -p topol.top -o em.tpr
>>> 
>>> Fatal error:
>>> Topology include file "   " not found
>>> For more information and tips for troubleshooting, please check the GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> 
>>> What is that mean?
>>> I thought maybe there is an invisible line so I did also dos2unix however 
>>> the error is still there.
>>> 
>> 
>> Are there any #include statements within your .itp files (e.g. 
>> cis-pinonic.itp) that might be triggering this?
>> 
>> -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.
> 

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Re: [gmx-users] Topology include file " " not found

2016-04-26 Thread gozde ergin

I checked it and there is no #include statement in cis-pinonic.itp file.
>  On 26 Apr 2016, at 13:24, Justin Lemkul  wrote:
> 
> 
> 
> On 4/26/16 5:57 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I am trying to simulate organic system.
>> Here is my tool.top file, and cis-pionic,its is in the same folder with the 
>> tool.top.
>> 
>> ;
>> ; Topology from .mol2 file
>> ; topolbuild
>> ;
>> ; The force field files to be included
>> #include "charmm27.ff/forcefield.itp"
>> 
>> ; Include chain topologies
>> #include “cis-pinonic.itp"
>> 
>> ; Include water topology
>> #include "charmm27.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 ]
>> ; title from mol2 input
>> LIG
>> 
>>  [ molecules ]
>> ; molecule namenr.
>>  cis-pinonic   64
>> 
>> 
>> When I try to minimize the system this is the error that I’m getting,
>> 
>> grompp -f minim.mdp  -c lig.gro -p topol.top -o em.tpr
>> 
>> Fatal error:
>> Topology include file "   " not found
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> 
>> What is that mean?
>> I thought maybe there is an invisible line so I did also dos2unix however 
>> the error is still there.
>> 
> 
> Are there any #include statements within your .itp files (e.g. 
> cis-pinonic.itp) that might be triggering this?
> 
> -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.

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Re: [gmx-users] Topology include file " " not found

2016-04-26 Thread Justin Lemkul




On 4/26/16 5:57 AM, gozde ergin wrote:

Dear all,

I am trying to simulate organic system.
Here is my tool.top file, and cis-pionic,its is in the same folder with the 
tool.top.

;
; Topology from .mol2 file
; topolbuild
;
; The force field files to be included
#include "charmm27.ff/forcefield.itp"

; Include chain topologies
#include “cis-pinonic.itp"

; Include water topology
#include "charmm27.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 ]
; title from mol2 input
LIG

  [ molecules ]
; molecule namenr.
  cis-pinonic   64


When I try to minimize the system this is the error that I’m getting,

grompp -f minim.mdp  -c lig.gro -p topol.top -o em.tpr

Fatal error:
Topology include file "   " not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

What is that mean?
I thought maybe there is an invisible line so I did also dos2unix however the 
error is still there.



Are there any #include statements within your .itp files (e.g. cis-pinonic.itp) 
that might be triggering this?


-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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* Please search the archive at 
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[gmx-users] Topology include file " " not found

2016-04-26 Thread gozde ergin

Dear all,

I am trying to simulate organic system.
Here is my tool.top file, and cis-pionic,its is in the same folder with the 
tool.top.

;
; Topology from .mol2 file
; topolbuild
;
; The force field files to be included
#include "charmm27.ff/forcefield.itp"

; Include chain topologies
#include “cis-pinonic.itp"   

; Include water topology
#include "charmm27.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 ]
; title from mol2 input
LIG

 [ molecules ]
; molecule namenr.
 cis-pinonic   64


When I try to minimize the system this is the error that I’m getting,

grompp -f minim.mdp  -c lig.gro -p topol.top -o em.tpr

Fatal error:
Topology include file "   " not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

What is that mean? 
I thought maybe there is an invisible line so I did also dos2unix however the 
error is still there.
-- 
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
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Re: [gmx-users] Topology include file " " not found

Re: [gmx-users] Topology include file " " not found

Re: [gmx-users] Topology include file " " not found

Re: [gmx-users] Topology include file " " not found

[gmx-users] Topology include file " " not found

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