Re: [gmx-users] Topolbuild

[Ray, Bruce D]

On Mar 21, 2018, at 10:15 AM, Alex <alexanderwie...@gmail.com> wrote:

> Date: Wed, 21 Mar 2018 09:47:06 -0400
> From: Alex <alexanderwie...@gmail.com>
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Topolbuild
> Message-ID:
>   

[gmx-users] Topolbuild

[Alex]

Dear all,

Using topolbuild the *.gro and *.top file for a GPS molecule (C_6H_14O_5Si)
were generated. In the GPS molecule there is a --Si(OH)3 group in which the
Si and H are indeed the atoms which produce problem in the topol file.
The Si and that H are named like below in the [ atom ] section ;

 [ atoms ]
;  nrtype   resnr   residu   atom   cgnrcharge  mass
1opls_154 1   GPS   O1   0.0  15.99940
;   0.000
2 H?? 1   GPS   H1   0.0   1.00800
;   0.000
3  SI 1   GPS  Si1   0.0  28.08000
;   0.000
4opls_136 1   GPS   C2   0.0  12.01100
;   0.000
5opls_140 1   GPS   H2   0.0   1.00800
;   0.000

And then the bond and angle sections wherever those two atoms are involved
are empty like below;
 [ bonds ]
;   ai  aj   funct  b0  kb
  2423   1 0.10880  284512.   ; H- C
  4 6   1 0.10900  284512.   ; C- H
   4 3; C-Si
  1413; H- O
  13 3; O-Si
   3 1;Si- O
   315;Si- O

Any suggestion to overcome the problem would be highly appreciated.

Best regards,
Alex
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Re: [gmx-users] TOPOLBUILD

[Ray, Bruce D]

On Apr 8, 2017, at 13:34:08 +0530 Vidya Devi  wrote:
 wrote:

> Hi gromacs users,
> 
> I am using topolbuild to generate oplsaa force field parameters.
> 
> ./topolbuild -n LIGAND.mol2 -dir
> C:/cygwin64/usr/local/gromacs/share/gromacs/top/oplsaa.ff -meas
> Need correct parameters
> 
>.
> 
> What should I do to get correct parameters?
> 
> Thanks,
> Vidya.R


The correct parameters are included with the topolbuild files.
In the topolbuild package, there is a directory called dat
Whereever you placed that directory is where the -dir parameter
should be pointed.  Ordinarily, one would run topolbuild in the
directory of the mol2 file from which the topology is to be built.
This ensures that the topology is built in the same directory as
the mol2 file and _not_ in the directory of the topolbuild binary.
Thus, for oplsaa, one would write a command that has a general form:
   /path_to_topolbuild/topolbuild -n LIGAND -dir 
/path_to_topolbuild_data/dat/gromacs -ff oplsaa
Note that the directory pointed to is a topolbuild directory and not
part of the gromacs distribution, and not to a specific forcefield
file.  This is because automatic topology generation needs more atom
typing information.

Examples of commands are given in the file PROGRAM_TESTING DONE.txt
General explanation of program commands is given in the file README.txt
Warnings about the limitations of automatic topology generation are
given in the file limitations.txt


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202


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Re: [gmx-users] TOPOLBUILD 1.3

[Ray, Bruce D]

> Date: Mon, 27 Feb 2017 07:26:23 +
> From: "Subashini .K" <subashi...@hotmail.com>
> To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
> Subject: [gmx-users] TOPOLBUILD 1.3
> Message-ID:
>   
> <sg2pr06mb1712153d90f961b3ff525873d4...@sg2pr06mb1712.apcprd06.prod.outlook.com>
>   
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi gromacs users,
> 
> 
> I want to use oplsaa force field for my organic compound.
> 
> 
> Can anyone tell me how to install topolbuild 1.3 and thereby generate .GRO, 
> .ITP and .TOP with opls-aa parameter incorporated in it?
> 
> 
> Thanks,
> 
> Subashini.K

Note that the source directory is in the directory "src'.

1. In the topolbuild source directory, change the defines in judge_types.h to 
read:
#define MAXLEVELS 16
#define MAXCHAIN 16
#define MAXENVBOND 16
#define MAXENVSTR 48
#define MAXSCAN 80
#define NULLCHAR 0
#define NUM_FEAT 25

2. In the source directory, follow the instructions in INSTALLATION.txt which 
reads:

INSTALLATION:
Compilation has been tested on a G4 Power Macintosh running Os X 10.3.9
with both gcc version 3.3  20030304 (Apple Computer, Inc. build 1671), 
and with gcc version 4.1.0 as distributed by the Fink Project.

Two make files, that may need editing for individual systems, are included
as follows:
 MakefileUses a standard C compiler with option -O
 to build the executable topolbuild
 Makefile.G4OsX  Optimization set for a G4 Power Macintosh
 running Os X with optimization options
 -O2 -mcpu=7450 -mtune=970
To build topolbuild, type
 make
If you happen to have a Mac PowerPC G4 running Mac OS X, you can also type
 make -f Makefile.G4OsX
Otherwise, your system may require editing of the make file according to
the specifications of your systems C compiler and libraries to generate a
functional program.  Advice on such editing is best gotten from your own
technical support people.

3.  To use, follow the instructions given in README.txt
The *.top generated will need to be correct for gromacs 3.3 and can be
converted for more recent gromacs versions with your favorite *NIX text 
editor.


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202


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[gmx-users] TOPOLBUILD 1.3

[Subashini .K]

Hi gromacs users,


I want to use oplsaa force field for my organic compound.


Can anyone tell me how to install topolbuild 1.3 and thereby generate .GRO, 
.ITP and .TOP with opls-aa parameter incorporated in it?


Thanks,

Subashini.K
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Re: [gmx-users] topolbuild ( Failing to read oxygen in H2O )

[Ray, Bruce D]

On Nov 28, 2016, at 9:26 PM,  <keisuke.o...@keio.jp> wrote:

> Date: Tue, 29 Nov 2016 11:26:08 +0900
> From:  <keisuke.o...@keio.jp>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] topolbuild ( Failing to read oxygen in H2O )
> Message-ID: <c1b704ef-958e-491a-a0a2-834994c1b...@keio.jp>
> Content-Type: text/plain; charset=utf-8
> 
> Dear Bruce D. Ray
> 
> 
> Thank you for replying to my question.
> 
> I understood that I should not include water molecules in submit file to 
> topolbuild
> because water topology is given by spce.itp.
> 
> Then, should I give coordinates of water to *.gro file and delete parameters 
> of water in topology file
> when hydrate structure is the object of my study? 
> 
> Sincerely.
> 
> 
> Keisuke Ohki
>> 2016/11/29 3:45?Ray, Bruce D <b...@iupui.edu>:
>> 
>> On Nov 26, 2016, at 4:19 AM,  <keisuke.o...@keio.jp> wrote:
>> 
>>> Date: Sat, 26 Nov 2016 17:24:56 +0900
>>> From:  <keisuke.o...@keio.jp>
>>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>>> Subject: [gmx-users]  topolbuild ( Failing to read oxygen in H2O )
>>> Message-ID: <07c401c0-1755-433c-9e89-c7a9e8a87...@keio.jp>
>>> Content-Type: text/plain; charset=us-ascii
>>> 
>>> Dear gromacs users
>>> 
>>> I have a question why topolbuild fails to read oxygen in H2O.
>>> 
>>> I want to make a topology file of methane hydrate structure with topolbuild 
>>> and run simulation in gromacs.
>>> 
>>> I used following command line:
>>> 
>>> ./topolbuild -n ../HYDRATE_A -dir ../dat/gromacs -ff oplsaa -purge 0
>>> 
>>> .mol2 file that I  used then { 
>>> 
>>> @MOLECULE
>>> ch4h2o_4.pdb
>>> 46 36 10 0 0
>>> SMALL
>>> USER_CHARGES
>>> 
>>> 
>>> @ATOM
>>>1 C   5.60601.66705.1720 C.3   1 LIG1   -0.4588
>>>2 H   6.23902.29905.8040 H 1 LIG10.1147
>>>3 H   4.97401.03505.8040 H 1 LIG10.1147
>>>4 H   4.97402.29904.5400 H 1 LIG10.1147
>>>5 H   6.23901.03504.5400 H 1 LIG10.1147
>>>  :
>>>   41 O   7.00601.71508.9340 O.3   9 H2O-1.1794
>>>   42 H   6.01301.71509.0510 H 9 H2O 0.5897
>>>   43 H   7.44401.71509.8330 H 9 H2O 0.5897
>>>   44 O   6.95701.72001.4090 O.3  10 H2O-1.1794
>>>   45 H   7.20500.87801.8880 H10 H2O 0.5897
>>>   46 H   7.24002.50801.9570 H10 H2O 0.5897
>>> @BOND
>>>   112 1
>>>   213 1
>>>   314 1
>>>   415 1
>>>   :
>>>  33   41   42 1
>>>  34   41   43 1
>>>  35   44   45 1
>>>  36   44   46 1
>>> @SUBSTRUCTURE
>>>   1 LIG1 1 RESIDUE   4 A LIG1 0 ROOT
>>>   2 LIG1 6 RESIDUE   4 A LIG1 0 ROOT
>>>   3 LIG111 RESIDUE   4 A LIG1 0 ROOT
>>>   4 LIG116 RESIDUE   4 A LIG1 0 ROOT
>>>   5 LIG121 RESIDUE   4 A LIG1 0 ROOT
>>>   6 LIG126 RESIDUE   4 A LIG1 0 ROOT
>>>   7 LIG131 RESIDUE   4 A LIG1 0 ROOT
>>>   8 LIG136 RESIDUE   4 A LIG1 0 ROOT
>>>   9 H2O41 RESIDUE   4 A H2O 0 ROOT
>>>  10 H2O44 RESIDUE   4 A H2O 0 ROOT
>>> 
>>> }
>>> 
>>> ( this file was used for trial, so this is not hydrate structure )
>>> 
>>> Then, I got this topology file {
>>> 
>>> ; The force field files to be included
>>> #include "ffHYDRATE_A.itp"
>>> 
>>> [ moleculetype ]
>>> ; name  nrexcl
>>> ch4h2o_4.pdb   3
>>> 
>>> [ atoms ]
>>> ;  nrtype   resnr   residu   atom   cgnrcharge  mass
>>>  1opls_138 1   LIG   C1  -0.45880  12.01100   ;  
>>> -0.4588000
>>>  2opls_140 1   LIG   H1   0.11470   1.00800   ;  
>>> -0.3441000
>>>  3opls_140 1   LIG   H1   0.11470   1.00800   ;  
>>> -0.2294000
>>>  4opls_140 1   LIG   H1   0.11470   1.00800   ;  
>>> -0.1147000
>>>  5opls_140 1  

Re: [gmx-users] topolbuild ( Failing to read oxygen in H2O )

[大木啓輔]

Dear Bruce D. Ray


Thank you for replying to my question.

I understood that I should not include water molecules in submit file to 
topolbuild
because water topology is given by spce.itp.

Then, should I give coordinates of water to *.gro file and delete parameters of 
water in topology file
when hydrate structure is the object of my study? 

Sincerely.


Keisuke Ohki
> 2016/11/29 3:45、Ray, Bruce D <b...@iupui.edu>のメール:
> 
> On Nov 26, 2016, at 4:19 AM,  <keisuke.o...@keio.jp> wrote:
> 
>> Date: Sat, 26 Nov 2016 17:24:56 +0900
>> From:  <keisuke.o...@keio.jp>
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: [gmx-users]  topolbuild ( Failing to read oxygen in H2O )
>> Message-ID: <07c401c0-1755-433c-9e89-c7a9e8a87...@keio.jp>
>> Content-Type: text/plain; charset=us-ascii
>> 
>> Dear gromacs users
>> 
>> I have a question why topolbuild fails to read oxygen in H2O.
>> 
>> I want to make a topology file of methane hydrate structure with topolbuild 
>> and run simulation in gromacs.
>> 
>> I used following command line:
>> 
>> ./topolbuild -n ../HYDRATE_A -dir ../dat/gromacs -ff oplsaa -purge 0
>> 
>> .mol2 file that I  used then { 
>> 
>> @MOLECULE
>> ch4h2o_4.pdb
>> 46 36 10 0 0
>> SMALL
>> USER_CHARGES
>> 
>> 
>> @ATOM
>> 1 C   5.60601.66705.1720 C.3   1 LIG1   -0.4588
>> 2 H   6.23902.29905.8040 H 1 LIG10.1147
>> 3 H   4.97401.03505.8040 H 1 LIG10.1147
>> 4 H   4.97402.29904.5400 H 1 LIG10.1147
>> 5 H   6.23901.03504.5400 H 1 LIG10.1147
>>   :
>>41 O   7.00601.71508.9340 O.3   9 H2O-1.1794
>>42 H   6.01301.71509.0510 H 9 H2O 0.5897
>>43 H   7.44401.71509.8330 H 9 H2O 0.5897
>>44 O   6.95701.72001.4090 O.3  10 H2O-1.1794
>>45 H   7.20500.87801.8880 H10 H2O 0.5897
>>46 H   7.24002.50801.9570 H10 H2O 0.5897
>> @BOND
>>112 1
>>213 1
>>314 1
>>415 1
>>:
>>   33   41   42 1
>>   34   41   43 1
>>   35   44   45 1
>>   36   44   46 1
>> @SUBSTRUCTURE
>>1 LIG1 1 RESIDUE   4 A LIG1 0 ROOT
>>2 LIG1 6 RESIDUE   4 A LIG1 0 ROOT
>>3 LIG111 RESIDUE   4 A LIG1 0 ROOT
>>4 LIG116 RESIDUE   4 A LIG1 0 ROOT
>>5 LIG121 RESIDUE   4 A LIG1 0 ROOT
>>6 LIG126 RESIDUE   4 A LIG1 0 ROOT
>>7 LIG131 RESIDUE   4 A LIG1 0 ROOT
>>8 LIG136 RESIDUE   4 A LIG1 0 ROOT
>>9 H2O41 RESIDUE   4 A H2O 0 ROOT
>>   10 H2O44 RESIDUE   4 A H2O 0 ROOT
>> 
>> }
>> 
>> ( this file was used for trial, so this is not hydrate structure )
>> 
>> Then, I got this topology file {
>> 
>> ; The force field files to be included
>> #include "ffHYDRATE_A.itp"
>> 
>> [ moleculetype ]
>> ; name  nrexcl
>> ch4h2o_4.pdb   3
>> 
>> [ atoms ]
>> ;  nrtype   resnr   residu   atom   cgnrcharge  mass
>>   1opls_138 1   LIG   C1  -0.45880  12.01100   ;  
>> -0.4588000
>>   2opls_140 1   LIG   H1   0.11470   1.00800   ;  
>> -0.3441000
>>   3opls_140 1   LIG   H1   0.11470   1.00800   ;  
>> -0.2294000
>>   4opls_140 1   LIG   H1   0.11470   1.00800   ;  
>> -0.1147000
>>   5opls_140 1   LIG   H1   0.11470   1.00800   ;   
>> 0.000
>>   :
>>  41 O?? 9   H2O   O9  -1.17940  15.99940   ;  
>> -1.1794000
>>  42opls_435 9   H2O   H   10   0.58970   1.00800   ;  
>> -0.5897000
>>  43opls_435 9   H2O   H   11   0.58970   1.00800   ;   
>> 0.000
>>  44 O??10   H2O   O   12  -1.17940  15.99940   ;  
>> -1.1794000
>>  45opls_43510   H2O   H   13   0.58970   1.00800   ;  
>> -0.5897000
>>  46opls_43510   H2O   H   14   0.58970   1.00800   ;   
>> 0.000
>> ; total molecule charge =   0.000
>> 
>> [ bonds ]
>> ;   a

Re: [gmx-users] topolbuild ( Failing to read oxygen in H2O )

[Ray, Bruce D]

On Nov 26, 2016, at 4:19 AM,  <keisuke.o...@keio.jp> wrote:

> Date: Sat, 26 Nov 2016 17:24:56 +0900
> From:  <keisuke.o...@keio.jp>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users]  topolbuild ( Failing to read oxygen in H2O )
> Message-ID: <07c401c0-1755-433c-9e89-c7a9e8a87...@keio.jp>
> Content-Type: text/plain; charset=us-ascii
> 
> Dear gromacs users
> 
> I have a question why topolbuild fails to read oxygen in H2O.
> 
> I want to make a topology file of methane hydrate structure with topolbuild 
> and run simulation in gromacs.
> 
> I used following command line:
> 
> ./topolbuild -n ../HYDRATE_A -dir ../dat/gromacs -ff oplsaa -purge 0
> 
> .mol2 file that I  used then { 
> 
> @MOLECULE
> ch4h2o_4.pdb
> 46 36 10 0 0
> SMALL
> USER_CHARGES
> 
> 
> @ATOM
>  1 C   5.60601.66705.1720 C.3   1 LIG1   -0.4588
>  2 H   6.23902.29905.8040 H 1 LIG10.1147
>  3 H   4.97401.03505.8040 H 1 LIG10.1147
>  4 H   4.97402.29904.5400 H 1 LIG10.1147
>  5 H   6.23901.03504.5400 H 1 LIG10.1147
>:
> 41 O   7.00601.71508.9340 O.3   9 H2O-1.1794
> 42 H   6.01301.71509.0510 H 9 H2O 0.5897
> 43 H   7.44401.71509.8330 H 9 H2O 0.5897
> 44 O   6.95701.72001.4090 O.3  10 H2O-1.1794
> 45 H   7.20500.87801.8880 H10 H2O 0.5897
> 46 H   7.24002.50801.9570 H10 H2O 0.5897
> @BOND
> 112 1
> 213 1
> 314 1
> 415 1
> :
>33   41   42 1
>34   41   43 1
>35   44   45 1
>36   44   46 1
> @SUBSTRUCTURE
> 1 LIG1 1 RESIDUE   4 A LIG1 0 ROOT
> 2 LIG1 6 RESIDUE   4 A LIG1 0 ROOT
> 3 LIG111 RESIDUE   4 A LIG1 0 ROOT
> 4 LIG116 RESIDUE   4 A LIG1 0 ROOT
> 5 LIG121 RESIDUE   4 A LIG1 0 ROOT
> 6 LIG126 RESIDUE   4 A LIG1 0 ROOT
> 7 LIG131 RESIDUE   4 A LIG1 0 ROOT
> 8 LIG136 RESIDUE   4 A LIG1 0 ROOT
> 9 H2O41 RESIDUE   4 A H2O 0 ROOT
>10 H2O44 RESIDUE   4 A H2O 0 ROOT
> 
> }
> 
> ( this file was used for trial, so this is not hydrate structure )
> 
> Then, I got this topology file {
> 
> ; The force field files to be included
> #include "ffHYDRATE_A.itp"
> 
> [ moleculetype ]
> ; name  nrexcl
> ch4h2o_4.pdb   3
> 
> [ atoms ]
> ;  nrtype   resnr   residu   atom   cgnrcharge  mass
>1opls_138 1   LIG   C1  -0.45880  12.01100   ;  
> -0.4588000
>2opls_140 1   LIG   H1   0.11470   1.00800   ;  
> -0.3441000
>3opls_140 1   LIG   H1   0.11470   1.00800   ;  
> -0.2294000
>4opls_140 1   LIG   H1   0.11470   1.00800   ;  
> -0.1147000
>5opls_140 1   LIG   H1   0.11470   1.00800   ;   
> 0.000
>:
>   41 O?? 9   H2O   O9  -1.17940  15.99940   ;  
> -1.1794000
>   42opls_435 9   H2O   H   10   0.58970   1.00800   ;  
> -0.5897000
>   43opls_435 9   H2O   H   11   0.58970   1.00800   ;   
> 0.000
>   44 O??10   H2O   O   12  -1.17940  15.99940   ;  
> -1.1794000
>   45opls_43510   H2O   H   13   0.58970   1.00800   ;  
> -0.5897000
>   46opls_43510   H2O   H   14   0.58970   1.00800   ;   
> 0.000
> ; total molecule charge =   0.000
> 
> [ bonds ]
> ;   ai  aj   funct  b0  kb
>   1 2   1 0.10900  284512.   ; C- H
>   1 3   1 0.10900  284512.   ; C- H
>   1 4   1 0.10900  284512.   ; C- H
>   1 5   1 0.10900  284512.   ; C- H
>   :
>  4142; O- H
>  4143; O- H
>  4445; O- H
>  4446; O- H
> 
> [ pairs ]
> 
> [ angles ]
> ; ai  aj  ak  funct  th0 cth
> 3 1 2   1 107.800276.1440 ; H- C- H
> 4 1 2   1 107.800276.1440 ; 

Re: [gmx-users] topolbuild ( Failing to read oxygen in H2O )

[大木啓輔]

Dear David van der Spoel


Thank you for giving me advice.

I'll choose TIP4P/Ice model and write its parameters on the topology files.

Sincerely.


Keisuke Ohki, senior student.
Dept. applied physics and physico-informatics., Keio University.

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Re: [gmx-users] topolbuild ( Failing to read oxygen in H2O )

[David van der Spoel]

On 26/11/16 09:24, 大木啓輔 wrote:

Dear gromacs users

I have a question why topolbuild fails to read oxygen in H2O.

I want to make a topology file of methane hydrate structure with topolbuild and 
run simulation in gromacs.

For these simple molecules you want hand-tuned force fields not 
automatically generated stuff. That mean writing the topologies your 
self, and choosing a standard water model, e.g. TIP4P or TIP4P/Ice for 
your application.



I used following command line:

./topolbuild -n ../HYDRATE_A -dir ../dat/gromacs -ff oplsaa -purge 0

.mol2 file that I  used then {

@MOLECULE
ch4h2o_4.pdb
46 36 10 0 0
SMALL
USER_CHARGES


@ATOM
  1 C   5.60601.66705.1720 C.3   1 LIG1   -0.4588
  2 H   6.23902.29905.8040 H 1 LIG10.1147
  3 H   4.97401.03505.8040 H 1 LIG10.1147
  4 H   4.97402.29904.5400 H 1 LIG10.1147
  5 H   6.23901.03504.5400 H 1 LIG10.1147
:
 41 O   7.00601.71508.9340 O.3   9 H2O-1.1794
 42 H   6.01301.71509.0510 H 9 H2O 0.5897
 43 H   7.44401.71509.8330 H 9 H2O 0.5897
 44 O   6.95701.72001.4090 O.3  10 H2O-1.1794
 45 H   7.20500.87801.8880 H10 H2O 0.5897
 46 H   7.24002.50801.9570 H10 H2O 0.5897
@BOND
 112 1
 213 1
 314 1
 415 1
 :
33   41   42 1
34   41   43 1
35   44   45 1
36   44   46 1
@SUBSTRUCTURE
 1 LIG1 1 RESIDUE   4 A LIG1 0 ROOT
 2 LIG1 6 RESIDUE   4 A LIG1 0 ROOT
 3 LIG111 RESIDUE   4 A LIG1 0 ROOT
 4 LIG116 RESIDUE   4 A LIG1 0 ROOT
 5 LIG121 RESIDUE   4 A LIG1 0 ROOT
 6 LIG126 RESIDUE   4 A LIG1 0 ROOT
 7 LIG131 RESIDUE   4 A LIG1 0 ROOT
 8 LIG136 RESIDUE   4 A LIG1 0 ROOT
 9 H2O41 RESIDUE   4 A H2O 0 ROOT
10 H2O44 RESIDUE   4 A H2O 0 ROOT

}

( this file was used for trial, so this is not hydrate structure )

Then, I got this topology file {

; The force field files to be included
#include "ffHYDRATE_A.itp"

 [ moleculetype ]
; name  nrexcl
ch4h2o_4.pdb   3

 [ atoms ]
;  nrtype   resnr   residu   atom   cgnrcharge  mass
1opls_138 1   LIG   C1  -0.45880  12.01100   ;  
-0.4588000
2opls_140 1   LIG   H1   0.11470   1.00800   ;  
-0.3441000
3opls_140 1   LIG   H1   0.11470   1.00800   ;  
-0.2294000
4opls_140 1   LIG   H1   0.11470   1.00800   ;  
-0.1147000
5opls_140 1   LIG   H1   0.11470   1.00800   ;   
0.000
:
   41 O?? 9   H2O   O9  -1.17940  15.99940   ;  
-1.1794000
   42opls_435 9   H2O   H   10   0.58970   1.00800   ;  
-0.5897000
   43opls_435 9   H2O   H   11   0.58970   1.00800   ;   
0.000
   44 O??10   H2O   O   12  -1.17940  15.99940   ;  
-1.1794000
   45opls_43510   H2O   H   13   0.58970   1.00800   ;  
-0.5897000
   46opls_43510   H2O   H   14   0.58970   1.00800   ;   
0.000
; total molecule charge =   0.000

 [ bonds ]
;   ai  aj   funct  b0  kb
   1 2   1 0.10900  284512.   ; C- H
   1 3   1 0.10900  284512.   ; C- H
   1 4   1 0.10900  284512.   ; C- H
   1 5   1 0.10900  284512.   ; C- H
   :
  4142; O- H
  4143; O- H
  4445; O- H
  4446; O- H

 [ pairs ]

[ angles ]
; ai  aj  ak  funct  th0 cth
 3 1 2   1 107.800276.1440 ; H- C- H
 4 1 2   1 107.800276.1440 ; H- C- H
 5 1 2   1 107.800276.1440 ; H- C- H
 :
434142 ; H- O- H
464445 ; H- O- H

}

I tried other input files with changing O.3 to (O.spc and H.spc) and (O.t3p and 
H.t3p) ,
but force field types of oxygen in H2O were not read.

Why this problem was occurred?
Should I fix this topology file?

Could you tell me this problem solution, please?








--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  

[gmx-users] topolbuild ( Failing to read oxygen in H2O )

[大木啓輔]

Dear gromacs users

I have a question why topolbuild fails to read oxygen in H2O.

I want to make a topology file of methane hydrate structure with topolbuild and 
run simulation in gromacs.

I used following command line:

./topolbuild -n ../HYDRATE_A -dir ../dat/gromacs -ff oplsaa -purge 0

.mol2 file that I  used then { 

@MOLECULE
ch4h2o_4.pdb
46 36 10 0 0
SMALL
USER_CHARGES


@ATOM
  1 C   5.60601.66705.1720 C.3   1 LIG1   -0.4588
  2 H   6.23902.29905.8040 H 1 LIG10.1147
  3 H   4.97401.03505.8040 H 1 LIG10.1147
  4 H   4.97402.29904.5400 H 1 LIG10.1147
  5 H   6.23901.03504.5400 H 1 LIG10.1147
:
 41 O   7.00601.71508.9340 O.3   9 H2O-1.1794
 42 H   6.01301.71509.0510 H 9 H2O 0.5897
 43 H   7.44401.71509.8330 H 9 H2O 0.5897
 44 O   6.95701.72001.4090 O.3  10 H2O-1.1794
 45 H   7.20500.87801.8880 H10 H2O 0.5897
 46 H   7.24002.50801.9570 H10 H2O 0.5897
@BOND
 112 1
 213 1
 314 1
 415 1
 :
33   41   42 1
34   41   43 1
35   44   45 1
36   44   46 1
@SUBSTRUCTURE
 1 LIG1 1 RESIDUE   4 A LIG1 0 ROOT
 2 LIG1 6 RESIDUE   4 A LIG1 0 ROOT
 3 LIG111 RESIDUE   4 A LIG1 0 ROOT
 4 LIG116 RESIDUE   4 A LIG1 0 ROOT
 5 LIG121 RESIDUE   4 A LIG1 0 ROOT
 6 LIG126 RESIDUE   4 A LIG1 0 ROOT
 7 LIG131 RESIDUE   4 A LIG1 0 ROOT
 8 LIG136 RESIDUE   4 A LIG1 0 ROOT
 9 H2O41 RESIDUE   4 A H2O 0 ROOT
10 H2O44 RESIDUE   4 A H2O 0 ROOT

}

( this file was used for trial, so this is not hydrate structure )

Then, I got this topology file {
 
; The force field files to be included
#include "ffHYDRATE_A.itp"

 [ moleculetype ]
; name  nrexcl
ch4h2o_4.pdb   3

 [ atoms ]
;  nrtype   resnr   residu   atom   cgnrcharge  mass
1opls_138 1   LIG   C1  -0.45880  12.01100   ;  
-0.4588000
2opls_140 1   LIG   H1   0.11470   1.00800   ;  
-0.3441000
3opls_140 1   LIG   H1   0.11470   1.00800   ;  
-0.2294000
4opls_140 1   LIG   H1   0.11470   1.00800   ;  
-0.1147000
5opls_140 1   LIG   H1   0.11470   1.00800   ;   
0.000
:
   41 O?? 9   H2O   O9  -1.17940  15.99940   ;  
-1.1794000
   42opls_435 9   H2O   H   10   0.58970   1.00800   ;  
-0.5897000
   43opls_435 9   H2O   H   11   0.58970   1.00800   ;   
0.000
   44 O??10   H2O   O   12  -1.17940  15.99940   ;  
-1.1794000
   45opls_43510   H2O   H   13   0.58970   1.00800   ;  
-0.5897000
   46opls_43510   H2O   H   14   0.58970   1.00800   ;   
0.000
; total molecule charge =   0.000

 [ bonds ]
;   ai  aj   funct  b0  kb
   1 2   1 0.10900  284512.   ; C- H
   1 3   1 0.10900  284512.   ; C- H
   1 4   1 0.10900  284512.   ; C- H
   1 5   1 0.10900  284512.   ; C- H
   :
  4142; O- H
  4143; O- H
  4445; O- H
  4446; O- H

 [ pairs ]

[ angles ]
; ai  aj  ak  funct  th0 cth
 3 1 2   1 107.800276.1440 ; H- C- H
 4 1 2   1 107.800276.1440 ; H- C- H
 5 1 2   1 107.800276.1440 ; H- C- H
 :
434142 ; H- O- H
464445 ; H- O- H

} 

I tried other input files with changing O.3 to (O.spc and H.spc) and (O.t3p and 
H.t3p) ,
but force field types of oxygen in H2O were not read. 

Why this problem was occurred? 
Should I fix this topology file? 

Could you tell me this problem solution, please?





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Re: [gmx-users] topolbuild error

[Ray, Bruce D]

On Feb 19, 2015, at 9:49 AM, Zahra Ghanbari, zahraghanbar...@gmail.com
wrote:

 hi
 I installed topolbuild version 1.3. I used following command line:
 ./topolbuild -dir /home/supermicro/topolbuild1_3/dat/gromacs -ff oplsaa -n
 OXL -r OXL -meas -rename -move
 I encountered with following error:
 *** Error in `./topolbuild': free(): invalid next size (fast):
 0x01b752a0 ***
 === Backtrace: =
 /lib/x86_64-linux-gnu/libc.so.6(+0x80996)[0x7f9fa8024996]
 ./topolbuild[0x40701c]
 ./topolbuild[0x40b01e]
 ./topolbuild[0x403226]
 /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f9fa7fc5de5]
 ./topolbuild[0x401059]
 === Memory map: 
 0040-0042c000 r-xp  08:01 2543
 /home/supermicro/topolbuild1_3/src/topolbuild
 0062b000-0062c000 r--p 0002b000 08:01 2543
 /home/supermicro/topolbuild1_3/src/topolbuild
 0062c000-0062d000 rw-p 0002c000 08:01 2543
 /home/supermicro/topolbuild1_3/src/topolbuild
 0062d000-0062e000 rw-p  00:00 0
 01b74000-01b95000 rw-p  00:00 0
 [heap]
 7f9fa7d8e000-7f9fa7da3000 r-xp  08:01 58458205
 /lib/x86_64-linux-gnu/libgcc_s.so.1
 7f9fa7da3000-7f9fa7fa2000 ---p 00015000 08:01 58458205
 /lib/x86_64-linux-gnu/libgcc_s.so.1
 7f9fa7fa2000-7f9fa7fa3000 r--p 00014000 08:01 58458205
 /lib/x86_64-linux-gnu/libgcc_s.so.1
 7f9fa7fa3000-7f9fa7fa4000 rw-p 00015000 08:01 58458205
 /lib/x86_64-linux-gnu/libgcc_s.so.1
 7f9fa7fa4000-7f9fa8161000 r-xp  08:01 58461967
 /lib/x86_64-linux-gnu/libc-2.17.so
 7f9fa8161000-7f9fa8361000 ---p 001bd000 08:01 58461967
 /lib/x86_64-linux-gnu/libc-2.17.so
 7f9fa8361000-7f9fa8365000 r--p 001bd000 08:01 58461967
 /lib/x86_64-linux-gnu/libc-2.17.so
 7f9fa8365000-7f9fa8367000 rw-p 001c1000 08:01 58461967
 /lib/x86_64-linux-gnu/libc-2.17.so
 7f9fa8367000-7f9fa836c000 rw-p  00:00 0
 7f9fa836c000-7f9fa846f000 r-xp  08:01 58462018
 /lib/x86_64-linux-gnu/libm-2.17.so
 7f9fa846f000-7f9fa866e000 ---p 00103000 08:01 58462018
 /lib/x86_64-linux-gnu/libm-2.17.so
 7f9fa866e000-7f9fa866f000 r--p 00102000 08:01 58462018
 /lib/x86_64-linux-gnu/libm-2.17.so
 7f9fa866f000-7f9fa867 rw-p 00103000 08:01 58462018
 /lib/x86_64-linux-gnu/libm-2.17.so
 7f9fa867-7f9fa8693000 r-xp  08:01 58461943
 /lib/x86_64-linux-gnu/ld-2.17.so
 7f9fa8874000-7f9fa8877000 rw-p  00:00 0
 7f9fa888e000-7f9fa8892000 rw-p  00:00 0
 7f9fa8892000-7f9fa8893000 r--p 00022000 08:01 58461943
 /lib/x86_64-linux-gnu/ld-2.17.so
 7f9fa8893000-7f9fa8895000 rw-p 00023000 08:01 58461943
 /lib/x86_64-linux-gnu/ld-2.17.so
 7fffd745-7fffd7471000 rw-p  00:00 0
 [stack]
 7fffd749a000-7fffd749c000 r-xp  00:00 0
 [vdso]
 ff60-ff601000 r-xp  00:00 0
 [vsyscall]
 Aborted (core dumped)
 how to resolve this problem?
 any help will highly appreciated.
 

This looks like a compilation problem.  The error message is not a topolbuild
error.  From what is shown, I cannot tell from where the call to free() was made
and cannot give further help until that can be determined.


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202



-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202


-- 
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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Re: [gmx-users] topolbuild error

[Ray, Bruce D]

On Feb 19, 2015, at 12:44 PM, Zahra Ghanbari zahraghanbar...@gmail.com wrote:


Dear Ray
I tried to use another .mol2 file. I use USCF chimera to save it.

@TRIPOSMOLECULE
OXL.pdb
6 5 1 0 0
SMALL
NO_CHARGES


@TRIPOSATOM
 1 C1 47.7640   52.0960   49.3000 C.2   1 OXL0.
 2 C2 48.9620   53.0060   49.8530 C.2   1 OXL0.
 3 O1 47.5730   51.0150   49.8280 O.co2 1 OXL0.
 4 O2 49.5800   52.4680   50.7770 O.co2 1 OXL0.
 5 O3 47.0570   52.5150   48.3410 O.co2 1 OXL0.
 6 O4 49.0630   54.1080   49.2490 O.co2 1 OXL0.
@TRIPOSBOND
112 2
213 2
315 2
424 2
526 2
@TRIPOSSUBSTRUCTURE
1 OXL 1 RESIDUE   4 A OXL 0 ROOT

Unfortunately, I confronted the new error:

Fatal error.
Source code file: readmol2.c, line: 419
File read to end without finding molecule record reading mol2 file.
I am looking forward to getting your guidance.

Interesting.  The only time I've seen that error arise is when there
were extraneous characters in the file, typically because the file
was made under Windows.  Running dos2unix on such files typically
removed the problem.

I've been busy and have not actually worked on topolbuild 1.3 since
early 2011.


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202


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Re: [gmx-users] topolbuild error

[Zahra Ghanbari]

Dear Ray
I tried to use another .mol2 file. I use USCF chimera to save it.

@TRIPOSMOLECULE
OXL.pdb
6 5 1 0 0
SMALL
NO_CHARGES


@TRIPOSATOM
  1 C1 47.7640   52.0960   49.3000 C.2   1 OXL0.
  2 C2 48.9620   53.0060   49.8530 C.2   1 OXL0.
  3 O1 47.5730   51.0150   49.8280 O.co2 1 OXL0.
  4 O2 49.5800   52.4680   50.7770 O.co2 1 OXL0.
  5 O3 47.0570   52.5150   48.3410 O.co2 1 OXL0.
  6 O4 49.0630   54.1080   49.2490 O.co2 1 OXL0.
@TRIPOSBOND
 112 2
 213 2
 315 2
 424 2
 526 2
@TRIPOSSUBSTRUCTURE
 1 OXL 1 RESIDUE   4 A OXL 0 ROOT

Unfortunately, I confronted the new error:

Fatal error.
Source code file: readmol2.c, line: 419
File read to end without finding molecule record reading mol2 file.
I am looking forward to getting your guidance.

On Thu, Feb 19, 2015 at 7:06 PM, Ray, Bruce D b...@iupui.edu wrote:


 On Feb 19, 2015, at 9:49 AM, Zahra Ghanbari, zahraghanbar...@gmail.com
 wrote:

  hi
  I installed topolbuild version 1.3. I used following command line:
  ./topolbuild -dir /home/supermicro/topolbuild1_3/dat/gromacs -ff oplsaa
 -n
  OXL -r OXL -meas -rename -move
  I encountered with following error:
  *** Error in `./topolbuild': free(): invalid next size (fast):
  0x01b752a0 ***
  === Backtrace: =
  /lib/x86_64-linux-gnu/libc.so.6(+0x80996)[0x7f9fa8024996]
  ./topolbuild[0x40701c]
  ./topolbuild[0x40b01e]
  ./topolbuild[0x403226]
  /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f9fa7fc5de5]
  ./topolbuild[0x401059]
  === Memory map: 
  0040-0042c000 r-xp  08:01 2543
  /home/supermicro/topolbuild1_3/src/topolbuild
  0062b000-0062c000 r--p 0002b000 08:01 2543
  /home/supermicro/topolbuild1_3/src/topolbuild
  0062c000-0062d000 rw-p 0002c000 08:01 2543
  /home/supermicro/topolbuild1_3/src/topolbuild
  0062d000-0062e000 rw-p  00:00 0
  01b74000-01b95000 rw-p  00:00 0
  [heap]
  7f9fa7d8e000-7f9fa7da3000 r-xp  08:01 58458205
  /lib/x86_64-linux-gnu/libgcc_s.so.1
  7f9fa7da3000-7f9fa7fa2000 ---p 00015000 08:01 58458205
  /lib/x86_64-linux-gnu/libgcc_s.so.1
  7f9fa7fa2000-7f9fa7fa3000 r--p 00014000 08:01 58458205
  /lib/x86_64-linux-gnu/libgcc_s.so.1
  7f9fa7fa3000-7f9fa7fa4000 rw-p 00015000 08:01 58458205
  /lib/x86_64-linux-gnu/libgcc_s.so.1
  7f9fa7fa4000-7f9fa8161000 r-xp  08:01 58461967
  /lib/x86_64-linux-gnu/libc-2.17.so
  7f9fa8161000-7f9fa8361000 ---p 001bd000 08:01 58461967
  /lib/x86_64-linux-gnu/libc-2.17.so
  7f9fa8361000-7f9fa8365000 r--p 001bd000 08:01 58461967
  /lib/x86_64-linux-gnu/libc-2.17.so
  7f9fa8365000-7f9fa8367000 rw-p 001c1000 08:01 58461967
  /lib/x86_64-linux-gnu/libc-2.17.so
  7f9fa8367000-7f9fa836c000 rw-p  00:00 0
  7f9fa836c000-7f9fa846f000 r-xp  08:01 58462018
  /lib/x86_64-linux-gnu/libm-2.17.so
  7f9fa846f000-7f9fa866e000 ---p 00103000 08:01 58462018
  /lib/x86_64-linux-gnu/libm-2.17.so
  7f9fa866e000-7f9fa866f000 r--p 00102000 08:01 58462018
  /lib/x86_64-linux-gnu/libm-2.17.so
  7f9fa866f000-7f9fa867 rw-p 00103000 08:01 58462018
  /lib/x86_64-linux-gnu/libm-2.17.so
  7f9fa867-7f9fa8693000 r-xp  08:01 58461943
  /lib/x86_64-linux-gnu/ld-2.17.so
  7f9fa8874000-7f9fa8877000 rw-p  00:00 0
  7f9fa888e000-7f9fa8892000 rw-p  00:00 0
  7f9fa8892000-7f9fa8893000 r--p 00022000 08:01 58461943
  /lib/x86_64-linux-gnu/ld-2.17.so
  7f9fa8893000-7f9fa8895000 rw-p 00023000 08:01 58461943
  /lib/x86_64-linux-gnu/ld-2.17.so
  7fffd745-7fffd7471000 rw-p  00:00 0
  [stack]
  7fffd749a000-7fffd749c000 r-xp  00:00 0
  [vdso]
  ff60-ff601000 r-xp  00:00 0
  [vsyscall]
  Aborted (core dumped)
  how to resolve this problem?
  any help will highly appreciated.
 

 This looks like a compilation problem.  The error message is not a
 topolbuild
 error.  From what is shown, I cannot tell from where the call to free()
 was made
 and cannot give further help until that can be determined.


 --
 Bruce D. Ray, Ph.D.
 Associate Scientist
 IUPUI
 Physics Dept.
 402 N. Blackford St., Rm. LD-061
 Indianapolis, IN  46202



 --
 Bruce D. Ray, Ph.D.
 Associate Scientist
 IUPUI
 Physics Dept.
 402 N. Blackford St., Rm. LD-061
 Indianapolis, IN  46202


 --
 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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[gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

[leila karami]

Dear gromacs users

I installed topolbuild version 1.3. I used following command line:

./topolbuild -n khob -dir ../dat/gromacs/ -ff gmx53a6.dat -meas

I encountered with following error:

Fatal error.
Source code file: readmol2.c, line: 162
Atomic symbol O2 in atom type not found.

How to resolve this problem?

Any help will highly appreciated.
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[gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

[leila karami]

my mol2file is as follows:

  @TRIPOSMOLECULE
C:\Users\scc\Desktop\22.pdb
 30 31 0 0 0
SMALL
GASTEIGER

@TRIPOSATOM
  1  O2 0.99910.0511   -0.0859 O2  1  C1 -0.2444
  2  C2 2.22660.0511   -0.0859 Car 1  C1  0.3522
  3  N3 2.87602.9655   -4.9849 Nar 1  C1 -0.1783
  4  C4 2.22662.3904   -4.0182 Car 1  C1  0.1230
  5  N4 0.83012.3904   -4.0182 Npl 1  C1 -0.3430
  6  C5 2.89811.7958   -3.0187 Car 1  C1 -0.0056
  7  C6 2.22661.2012   -2.0192 Car 1  C1  0.0152
  8  N1 2.87600.6262   -1.0526 Nar 1  C1 -0.2700
  9  C1*4.31050.6262   -1.0526 C3  1  C1  0.1680
 10  H1*4.66721.1419   -1.9196 H   1  C1  0.0867
 11  O4*6.2372   -0.7744   -3.5532 O3  1  C1 -0.3456
 12  C4*4.8172   -0.7744   -3.5532 C3  1  C1  0.1126
 13  H4*4.4605   -1.2673   -4.4334 H   1  C1  0.0647
 14  C3*4.3105   -1.5070   -2.3216 C3  1  C1  0.1135
 15  H3*3.2405   -1.5070   -2.3216 H   1  C1  0.0647
 16  O3*4.7839   -2.8457   -2.3391 O3  1  C1 -0.3864
 17  C2*4.8172   -0.8068   -1.0713 C3  1  C1  0.1286
 18  H2*5.8872   -0.8068   -1.0713 H   1  C1  0.0665
 19  O2*4.3439   -1.49130.0793 O3  1  C1 -0.3847
 20  C5*4.31050.6586   -3.5345 C3  1  C1  0.0730
 21  O5*2.89050.6586   -3.5345 O3  1  C1 -0.3924
 22  H410.33011.9477   -3.2739 H   1  C1  0.1437
 23  H420.33012.8332   -4.7625 H   1  C1  0.1437
 24  H5 3.93011.7958   -3.0187 H   1  C1  0.0666
 25  H6 1.19461.2012   -2.0192 H   1  C1  0.0812
 26  H3*5.7839   -2.8457   -2.3391 HO  1  C1  0.2100
 27  H2*4.6772   -2.43400.0670 HO  1  C1  0.2101
 28 H5*14.66721.1515   -2.6543 H   1  C1  0.0584
 29 H5*24.66721.1743   -4.4015 H   1  C1  0.0584
 30  H5*2.55720.1979   -4.3571 HO  1  C1  0.2095
@TRIPOSBOND
 1 1 22
 2 2 3   ar
 3 2 8   ar
 4 3 4   ar
 5 4 51
 6 4 6   ar
 7 5221
 8 5231
 9 6 7   ar
10 6241
11 7 8   ar
12 7251
13 8 91
14 9111
15 9171
16 9101
1711121
1812131
1912141
2012201
2114171
2214161
2314151
2416261
2517181
2617191
2719271
2820211
2920281
3020291
3121301 leilakar...@dena.kntu.ac.ir
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[gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

[leila karami]

my mol2file is as follows:

  @TRIPOSMOLECULE
C:\Users\scc\Desktop\22.pdb
 30 31 0 0 0
SMALL
GASTEIGER

@TRIPOSATOM
  1  O2 0.99910.0511   -0.0859 O2  1  C1 -0.2444
  2  C2 2.22660.0511   -0.0859 Car 1  C1  0.3522
  3  N3 2.87602.9655   -4.9849 Nar 1  C1 -0.1783
  4  C4 2.22662.3904   -4.0182 Car 1  C1  0.1230
  5  N4 0.83012.3904   -4.0182 Npl 1  C1 -0.3430
  6  C5 2.89811.7958   -3.0187 Car 1  C1 -0.0056
  7  C6 2.22661.2012   -2.0192 Car 1  C1  0.0152
  8  N1 2.87600.6262   -1.0526 Nar 1  C1 -0.2700
  9  C1*4.31050.6262   -1.0526 C3  1  C1  0.1680
 10  H1*4.66721.1419   -1.9196 H   1  C1  0.0867
 11  O4*6.2372   -0.7744   -3.5532 O3  1  C1 -0.3456
 12  C4*4.8172   -0.7744   -3.5532 C3  1  C1  0.1126
 13  H4*4.4605   -1.2673   -4.4334 H   1  C1  0.0647
 14  C3*4.3105   -1.5070   -2.3216 C3  1  C1  0.1135
 15  H3*3.2405   -1.5070   -2.3216 H   1  C1  0.0647
 16  O3*4.7839   -2.8457   -2.3391 O3  1  C1 -0.3864
 17  C2*4.8172   -0.8068   -1.0713 C3  1  C1  0.1286
 18  H2*5.8872   -0.8068   -1.0713 H   1  C1  0.0665
 19  O2*4.3439   -1.49130.0793 O3  1  C1 -0.3847
 20  C5*4.31050.6586   -3.5345 C3  1  C1  0.0730
 21  O5*2.89050.6586   -3.5345 O3  1  C1 -0.3924
 22  H410.33011.9477   -3.2739 H   1  C1  0.1437
 23  H420.33012.8332   -4.7625 H   1  C1  0.1437
 24  H5 3.93011.7958   -3.0187 H   1  C1  0.0666
 25  H6 1.19461.2012   -2.0192 H   1  C1  0.0812
 26  H3*5.7839   -2.8457   -2.3391 HO  1  C1  0.2100
 27  H2*4.6772   -2.43400.0670 HO  1  C1  0.2101
 28 H5*14.66721.1515   -2.6543 H   1  C1  0.0584
 29 H5*24.66721.1743   -4.4015 H   1  C1  0.0584
 30  H5*2.55720.1979   -4.3571 HO  1  C1  0.2095
@TRIPOSBOND
 1 1 22
 2 2 3   ar
 3 2 8   ar
 4 3 4   ar
 5 4 51
 6 4 6   ar
 7 5221
 8 5231
 9 6 7   ar
10 6241
11 7 8   ar
12 7251
13 8 91
14 9111
15 9171
16 9101
1711121
1812131
1912141
2012201
2114171
2214161
2314151
2416261
2517181
2617191
2719271
2820211
2920281
3020291
3121301
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[gmx-users] topolbuild

[marzieh dehghan]

Hi

I used topolbuild to create topology file for glycated insulin, but there
are several dihedral parameters which are empty in output file. in order to
complete output file, several servers were used such as ATB, vienna, 
unfortunately none of them couldn't help me.

I would like to know how can I solve this problem to generate a complete
topology file.

thanks in advances

best wishes

-- 




*Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and
Biophysics (IBB)University of Tehran, Tehran- Iran.*
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Re: [gmx-users] topolbuild

[Bruce D. Ray]

On Sunday, May 4, 2014, at 3:04 AM Hossein Lanjanian 
hossein.lanjan...@gmail.com wrote:

 hi
 We installed topolbuild
 
 topolbuild version 1.3
 Command line:
      /home/Hossein/Desktop/topolbuild1_3/src/topolbuild -n test -dir
 ./topolbuild1_3/dat/gromacs -ff oplsaa
 
 Fatal error.
 Source code file: readmol2.c, line: 639
 Incomplete mol2 file after bonds record.:
 
 we would like to know, what is the origin of this error.
 -- 
 With The Best
 H.Lanjanian
 ---
 Hossein Lanjanian,
 Ph.D. student
 
 Laboratory of Systems Biology and Bioinformatics
 (LBB)
 Institute of Biochemistry and Biophysics (IBB), University of
 Tehran
 Tehran, Iran
 http://LBB.ut.ac.ir     http://ibb.ut.ac.ir
 h.lanjan...@ut.ac.ir
 

Your mol2 file does not have any mol2 lines after the bonds
records.  At the end of the bonds list, a proper mol2 file
has a line that begins with, @TRIPOS and ends with the
unix end of line.  For most mol2 files, this is line reads,
@TRIPOSSUBSTRUCTURE, but unless the mol2 file header
record calls for some form of restraints, the program only
checks for the initial tag.  To correct your file, you
only need to add the appropriate line, terminated by an
end of line, to your file.

I hope that helps. 

-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
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Re: [gmx-users] topolbuild error (marzieh dehghan)

[Justin Lemkul]

Please don't reply to the whole digest, and remember to use a sensible subject 
line.

On 5/5/14, 3:20 AM, marzieh dehghan wrote:

  Dear Justin Lemkul

Hi

  thank you for your kind answer

according to your advice, we changed #include fftest.itp to #include
oplsaa.ff/fftest.itp in the test.top.

fftest.itp contains the following cases:

; topolbuild version 1.3
; Command line:
; /home/Hossein/Desktop/topolbuild1_3/src/topolbuild -n test -dir
/home/Hossein/Desktop/topolbuild1_3/dat/gromacs -ff oplsaa
;
#define _FF_OPLS
#define _FF_OPLSAA
#define _FF_USER

[ defaults ]
;nbfunc comb-rule  gen-pairs fudgeLJ  fudgeQQ
   1   3   yes 0.5 0.5

#include ffoplsaanb.itp


  test.top contains the following cases:

;
; Topology from .mol2 file
; topolbuild version 1.3
; Command line:
; /home/Hossein/Desktop/topolbuild1_3/src/topolbuild -n test -dir
/home/Hossein/Desktop/topolbuild1_3/dat/gromacs -ff oplsaa
;
; The force field files to be included
#include oplsaa.ff/fftest.itp

  [ moleculetype ]
; name  nrexcl
insulin2.pdb   3

unfortunately after writing grompp -f ions.mdp -c test.gro -p test.top -o
ions.tpr

I confronted the new error topology include file oplsaa.ff/fftest.itp
not found





I am looking forward to getting your guidance.



OK, so let's back up.  You've got a modified force field that tries to use 
parameters from OPLS-AA.  So of course fftest.itp is not going to exist in the 
stock oplsaa.ff directory unless you moved it there.  The important point is 
that ffoplsaanb.itp does not exist and has not been named that for several 
years.  If your fftest.itp needs those parameters, then the #include statement 
in fftest.itp needs to be changed to #include oplsaa.ff/ffnonbonded.itp


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] topolbuild

[Hossein Lanjanian]

hi
We installed topolbuild

topolbuild version 1.3
Command line:
 /home/Hossein/Desktop/topolbuild1_3/src/topolbuild -n test -dir
./topolbuild1_3/dat/gromacs -ff oplsaa

Fatal error.
Source code file: readmol2.c, line: 639
Incomplete mol2 file after bonds record.:

we would like to know, what is the origin of this error.
-- 
With The Best
H.Lanjanian
---
Hossein Lanjanian,
Ph.D. student

Laboratory of Systems Biology and Bioinformatics
(LBB)
Institute of Biochemistry and Biophysics (IBB), University of
Tehran
Tehran, Iran
http://LBB.ut.ac.ir http://ibb.ut.ac.ir
h.lanjan...@ut.ac.ir

-
-
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