Re: [gmx-users] Invalid order for directive defaults

2013-11-13 Thread Justin Lemkul



On 11/13/13 11:53 AM, Atila Petrosian wrote:

Dear Justin

Thanks for your quick reply.

I was confused.

If I add #include "ffcntbon.itp" after #include "cnt.itp" in .top file,
my problem was solved and error was solved?



No.  The parameters are at the force field level and thus have to be #included 
before any [moleculetype] is introduced (see Chapter 5 of the manual for 
required order of directives).  If you do:


#include "charmm27.ff/forcefield.itp"
#include "ffcntbon.itp"

you should be fine.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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[gmx-users] Invalid order for directive defaults

2013-11-13 Thread Atila Petrosian
Dear Justin

Thanks for your quick reply.

I was confused.

If I add #include "ffcntbon.itp" after #include "cnt.itp" in .top file,
my problem was solved and error was solved?
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Re: [gmx-users] Invalid order for directive defaults

2013-11-13 Thread Justin Lemkul



On 11/13/13 10:39 AM, Atila Petrosian wrote:

Dear Justin

Thanks for your reply.


In your previous setup, you were effectively trying to use CHARMM27 + some other
force field related to the CNT.  You can't do that.


Thus, Gromacs is not appropriate for systems containing cnt.
Is my deduction true?



Of course not.  People simulate CNTs with Gromacs all the time.  You just didn't 
construct the force field properly.



In my case, peptid + cnt + water molecules, what is your suggestion?

Please guide me and explain more. How to do MD simulation of my system
by gromacs?



You have missing parameters in the .top/.itp file.  You have those parameters 
already in ffbonded.itp for the CNT.  As long as those parameters are compatible 
with the peptide force field (CHARMM27), then you just need to add those 
parameters.  Again, that may be as simple as adding #include "cntffbonded.itp" 
of whatever it is to the .top file after the #include statement for the parent 
force field.  Your only problem was #including another force field that 
re-defined a [defaults] directive.  That is syntactically illegal.  Nothing else 
was inherently problematic, unless you're mixing incompatible force fields, but 
I haven't seen any evidence of that.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Invalid order for directive defaults

2013-11-13 Thread Atila Petrosian
Dear Justin

Thanks for your reply.

> In your previous setup, you were effectively trying to use CHARMM27 + some 
> other
> force field related to the CNT.  You can't do that.

Thus, Gromacs is not appropriate for systems containing cnt.
Is my deduction true?

In my case, peptid + cnt + water molecules, what is your suggestion?

Please guide me and explain more. How to do MD simulation of my system
by gromacs?

Any help will highly appreciated.
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Re: [gmx-users] Invalid order for directive defaults

2013-11-13 Thread Justin Lemkul



On 11/13/13 5:51 AM, Atila Petrosian wrote:

Dear Justin

Very thanks for your reply.

I created a new topol.top file as below:

1) I used once default directive.

2) I put cnt.itp file in working directory.

3) I copied pr.top and renamed it to topol.top. I added #include "cnt.itp"
in the end of topol.top file. I modified [ molecules ] directive.
--
begining of topol.top file is as follows:

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

[ moleculetype ]
; Namenrexcl
Protein_chain_A 3

[ atoms ]
.
.
.
.

end of com.top file is as follows:

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

#include "cnt.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 ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
CNT 1
SOL  1388
---
Previous error (Invalid order for directive defaults) was solved, but
When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr,
I encountered with this error:

ERROR1 [file cnt.itp, line 2861]:
   No default Angle types
.
.
.
.
.
.

ERROR 1218 [file cnt.itp, line 4078]:
   No default Angle types

Fatal error:
There were 1218 errors in input file(s).


Lines 2861-4078 are related to [ angles ] directive in cnt.itp file.

How to solve this issue?



In your previous setup, you were effectively trying to use CHARMM27 + some other 
force field related to the CNT.  You can't do that.  What you can do (and need 
to do) is incorporate the nonbonded and bonded parameters related to the CNT 
into the parent force field.  You may be able to simply #include the 
ffnonbonded.itp and ffbonded.itp files in the topology.  Your current approach 
has simply deleted necessary information.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Invalid order for directive defaults

2013-11-13 Thread Atila Petrosian
Dear Justin

My cnt is infinite.

I obtained cnt.top by g_x2top and then modified cnt.top to cnt.itp.

For obtaining cnt.top, I used following files:
---
ffcnt.atp:

CA  12.01100 ;  aromatic C
---
ffcnt.n2t:

CCA0.0012.011  3C 0.141   C 0.141   C 0.141
CCA0.0012.011  2C 0.141   C 0.141
---
ffcntbon.itp:

[ bondtypes ]
; i j   funcb0  kb
CA  CA  3   0.1418   47890.0   21.867

[ angletypes ]
; i j   k   functh0 cth ub0 cub
CA  CA  CA  2   120.00  562.20

[ dihedraltypes ]
; i j   k   l   funcphi0cp  mult
CA  CA  CA  CA  5  0.00 25.12 0.00 0.00
---
ffcntnonbon.itp:

[ atomtypes ]
;name   at.num  masscharge  ptype   sigma   epsi
CA  6   12.011000.00A   0.385   0.4396
---
In cnt.itp file, angle section of file is as follows:

[ angles ]
;  aiajak functc0c1c2c3
2 1 8 1
2 1   287 1
8 1   287 1
1 2 3 1
1 210 1
3 210 1
2 3   289 1
2 3   406 1
  289 3   406 1
5 417 1
5 4   320 1
   17 4   320 1
4 5 6 1
.
.
.
.
.
.

I saw system.gro file by VMD, there are all angles defined above in
[angle] directive.
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[gmx-users] Invalid order for directive defaults

2013-11-13 Thread Atila Petrosian
Dear Justin

Very thanks for your reply.

I created a new topol.top file as below:

1) I used once default directive.

2) I put cnt.itp file in working directory.

3) I copied pr.top and renamed it to topol.top. I added #include "cnt.itp"
in the end of topol.top file. I modified [ molecules ] directive.
--
begining of topol.top file is as follows:

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

[ moleculetype ]
; Namenrexcl
Protein_chain_A 3

[ atoms ]
.
.
.
.

end of com.top file is as follows:

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

#include "cnt.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 ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
CNT 1
SOL  1388
---
Previous error (Invalid order for directive defaults) was solved, but
When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr,
I encountered with this error:

ERROR1 [file cnt.itp, line 2861]:
  No default Angle types
.
.
.
.
.
.

ERROR 1218 [file cnt.itp, line 4078]:
  No default Angle types

Fatal error:
There were 1218 errors in input file(s).


Lines 2861-4078 are related to [ angles ] directive in cnt.itp file.

How to solve this issue?

Any help will highly appreciated.
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Re: [gmx-users] Invalid order for directive defaults

2013-11-12 Thread Justin Lemkul



On 11/12/13 10:07 AM, Atila Petrosian wrote:

Dear all

My system contains protein + cnt + water molecules.

I have summarized what I did below:
---

1) By pdb2gmx and charmm27 force field, I obtained pr.top for protein then
I converted it into pr.itp by deleting

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

from begining of file and by deleting

; 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 ]
; Name
Protein

[ molecules ]
; Compound#mols
Protein_chain_A 1

from ending of file.


2) I used bonded and nonbonded parameters for cnt from paper:
  J. Phys. Chem. B 2001, 105, 9980-9987
(Carbon Nanotubes in Water: Structural Characteristics and Energetics).
I created cnt.ff folder containing following files:

ffcnt.atp / ffcnt.n2t / ffcnt.rtp / ffcntbon.itp / ffcntnonbon.itp /
forcefield.itp

Then, I put cnt.ff folder in GMXLIB directory.


3) By g_x2top and cnt.ff created in previous step, I obtained cnt.top for
cnt then I converted it into cnt.itp by deleting

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

from begining of file and by deleting

[ system ]
; Name
CNT

[ molecules ]
; Compound#mols
CNT 1

from ending of file.


4) I combined cnt and protein to create one coordination file (system.gro).
Order of molecules are as follows: 1) cnt 2) protein
3) water.


5) I wrote a topol.top file given below,

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

#include "cnt.itp"

#include "charmm27.ff/forcefield.itp"

#include "pr.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; 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 ]
; Name
CNT/Protein/SOL

[ molecules ]
; Compound#mols
CNT  1
Protein  1
SOL   1359


When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr, I
encountered with following error:

Fatal error:
Syntax error - File forcefield.itp, line 11
Last line read:
'[ defaults ]'
Invalid order for directive defaults

Content of forcefield.itp in cnt.ff directory is as follows:

***
*CHARMM port writted
by   *
*Par Bjelkmar, Per Larsson, Michel
Cuendet,   *
*Berk Hess and Erik
Lindahl.  *
*
Correspondance:  *
*bjelk...@cbr.su.se or lind...@cbr.su.se
*
***


#define _FF_CNT
[ defaults ]
; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ
12yes1.01.0

#include "ffcntnonbon.itp"
#include "ffcntbon.itp"

and

Content of forcefield.itp in Charmm27.ff directory is as follows:

***
*CHARMM port writted
by   *
*Par Bjelkmar, Per Larsson, Michel
Cuendet,   *
*Berk Hess and Erik
Lindahl.  *
*
Correspondance:  *
*bjelk...@cbr.su.se or lind...@cbr.su.se
*
***


#define _FF_CHARMM
[ defaults ]
; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ
12yes1.01.0

#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "gb.itp"
#include "cmap.itp"
; Nucleic acids nonbonded and bonded parameters"
#include "ffnanonbonded.itp"
#include "ffnabonded.itp"


In both of forcefield.itp files, line 11 is [ defaults ].

I changed name of  forcefield.itp file in cnt.ff directory to cntff.itp,
but there is same error, again.

That is all what I exactly did. Is

[gmx-users] Invalid order for directive defaults

2013-11-12 Thread Atila Petrosian
Dear all

My system contains protein + cnt + water molecules.

I have summarized what I did below:
---

1) By pdb2gmx and charmm27 force field, I obtained pr.top for protein then
I converted it into pr.itp by deleting

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

from begining of file and by deleting

; 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 ]
; Name
Protein

[ molecules ]
; Compound#mols
Protein_chain_A 1

from ending of file.


2) I used bonded and nonbonded parameters for cnt from paper:
 J. Phys. Chem. B 2001, 105, 9980-9987
(Carbon Nanotubes in Water: Structural Characteristics and Energetics).
I created cnt.ff folder containing following files:

ffcnt.atp / ffcnt.n2t / ffcnt.rtp / ffcntbon.itp / ffcntnonbon.itp /
forcefield.itp

Then, I put cnt.ff folder in GMXLIB directory.


3) By g_x2top and cnt.ff created in previous step, I obtained cnt.top for
cnt then I converted it into cnt.itp by deleting

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

from begining of file and by deleting

[ system ]
; Name
CNT

[ molecules ]
; Compound#mols
CNT 1

from ending of file.


4) I combined cnt and protein to create one coordination file (system.gro).
Order of molecules are as follows: 1) cnt 2) protein
3) water.


5) I wrote a topol.top file given below,

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

#include "cnt.itp"

#include "charmm27.ff/forcefield.itp"

#include "pr.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; 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 ]
; Name
CNT/Protein/SOL

[ molecules ]
; Compound#mols
CNT  1
Protein  1
SOL   1359


When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr, I
encountered with following error:

Fatal error:
Syntax error - File forcefield.itp, line 11
Last line read:
'[ defaults ]'
Invalid order for directive defaults

Content of forcefield.itp in cnt.ff directory is as follows:

***
*CHARMM port writted
by   *
*Par Bjelkmar, Per Larsson, Michel
Cuendet,   *
*Berk Hess and Erik
Lindahl.  *
*
Correspondance:  *
*bjelk...@cbr.su.se or lind...@cbr.su.se
*
***


#define _FF_CNT
[ defaults ]
; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ
12yes1.01.0

#include "ffcntnonbon.itp"
#include "ffcntbon.itp"

and

Content of forcefield.itp in Charmm27.ff directory is as follows:

***
*CHARMM port writted
by   *
*Par Bjelkmar, Per Larsson, Michel
Cuendet,   *
*Berk Hess and Erik
Lindahl.  *
*
Correspondance:  *
*bjelk...@cbr.su.se or lind...@cbr.su.se
*
***


#define _FF_CHARMM
[ defaults ]
; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ
12yes1.01.0

#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "gb.itp"
#include "cmap.itp"
; Nucleic acids nonbonded and bonded parameters"
#include "ffnanonbonded.itp"
#include "ffnabonded.itp"


In both of forcefield.itp files, line 11 is [ defaults ].

I changed name of  forcefield.itp file in cnt.ff directory to cntff.itp,
but there is same error, again.

That is all what I exactly did. Is anything wrong or missing?
How to solve this error?

Re: [gmx-users] Invalid order for directive defaults

2008-01-11 Thread Mark Abraham



Fatal error:
Invalid order for directive defaults, file 
""/panfs/storage.local/scs/home/myunggi/gromacs-openmpi/share/gromacs/top/ffgmx.itp"", 
line 4



I think I have only one [ defaults ] section.
Does Anybody have an idea? What is wrong?


Check out 
http://wiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults


Mark
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[gmx-users] Invalid order for directive defaults

2008-01-11 Thread Myunggi Yi
Dear gromca users,

I'm a new user of gromacs.
I'm trying to run energy minimization on the system of a short peptide and a
lipid bilayer.
The following is my top file.


;
#include "ffgmx.itp"
#include "../lipid.popc.itp"
#include "popc.itp"
#include "pro.itp"
#include "ions.itp"
#include "spc.itp"


[ system ]
; name
Fusion peptide on POPC

[ molecules ]
; name  number
Protein 1
POPC128
Na  2
SOL 3655
+++



And I copied em.mdp with a little modification from the tutorial.



+++
;   User spoel (236)
;   Wed Nov  3 17:12:44 1993
;   Input file
;
cpp =  cpp
define  =  -DPOSRES
constraints =  none
integrator  =  steep
nsteps  =  100
;
;   Energy minimizing stuff
;
emtol   =  2000
emstep  =  0.01

nstcomm =  1
ns_type =  grid
rlist   =  1
rcoulomb=  1.0
rvdw=  1.0
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no
++


After runing grompp I've got the following error message.


++
Program grompp, VERSION 3.3.1
Source code file: topio.c, line: 388

Fatal error:
Invalid order for directive defaults, file
""/panfs/storage.local/scs/home/myunggi/gromacs-openmpi/share/gromacs/top/ffgmx.itp"",
line 4


I think I have only one [ defaults ] section.
Does Anybody have an idea? What is wrong?

Have a great day.


-- 
Best wishes,

MYUNGGI YI
==
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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