[gmx-users] itp problem

2013-08-17 Thread Albert 

Hello:

 I am trying to restrain part  of my protein. First I generate a index 
file by make_ndx. Then I use genrest for this purpose like:


genres -f npt.gro -o helix -n -fc 400

after that I change the following in the topol.top file, like:


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

when I run grompp, it claimed following warnings:

WARNING 1 [file helix.itp, line 1]:
  Too few parameters on line (source file
  /home/albert/install/source/gromacs-4.6.3/src/kernel/toppush.c, line 
1756)


here is my helix.itp:
; position restraints for System of

[ position_restraints ]
;  i funct   fcxfcyfcz
   51400400400
  241400400400
  411400400400
  481400400400
  591400400400
  701400400400
  861400400400
 1071400400400
 1261400400400
 1401400400400
 1561400400400
 1711400400400
 1901400400400
 2001400400400
 2191400400400
 2291400400400
 2451400400400
 2641400400400
 2741400400400


thank you very much.
Albert


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Re: [gmx-users] generation of gro file

2013-08-17 Thread Musharaf Ali 
Dear Justin
Again thanks. Actually the problem arises in the running of pdb2gmx of pdb
file of crown ether. I have generated the pdb file from xyz coordinates
using openbabel. The pdb file looks like below.


COMPND D:\data-structure\18c6.xyz

AUTHOR GENERATED BY OPEN BABEL 2.3.2

HETATM 1 O LIG 1 0.000 0.000 0.000 1.00 0.00 O

HETATM 2 C LIG 1 0.000 0.000 1.400 1.00 0.00 C

HETATM 3 C LIG 1 1.367 0.000 1.883 1.00 0.00 C

HETATM 4 H LIG 1 -0.513 0.889 1.763 1.00 0.00 H

HETATM 5 H LIG 1 -0.513 -0.889 1.763 1.00 0.00 H

HETATM 6 H LIG 1 1.367 0.000 2.972 1.00 0.00 H

HETATM 7 O LIG 1 2.027 -1.143 1.417 1.00 0.00 O

HETATM 8 H LIG 1 1.880 0.889 1.520 1.00 0.00 H

HETATM 9 C LIG 1 3.347 -1.143 1.883 1.00 0.00 C

HETATM 10 C LIG 1 4.031 -2.327 1.400 1.00 0.00 C

HETATM 11 H LIG 1 3.860 -0.254 1.520 1.00 0.00 H

HETATM 12 H LIG 1 3.347 -1.143 2.972 1.00 0.00 H

HETATM 13 H LIG 1 5.057 -2.327 1.763 1.00 0.00 H

HETATM 14 H LIG 1 3.517 -3.216 1.763 1.00 0.00 H

HETATM 15 O LIG 1 4.031 -2.327 -0.000 1.00 0.00 O

HETATM 16 C LIG 1 4.690 -3.470 -0.467 1.00 0.00 C

HETATM 17 C LIG 1 4.690 -3.470 -1.917 1.00 0.00 C

HETATM 18 H LIG 1 5.717 -3.470 -0.104 1.00 0.00 H

HETATM 19 H LIG 1 4.177 -4.359 -0.104 1.00 0.00 H

HETATM 20 H LIG 1 5.204 -4.359 -2.280 1.00 0.00 H

HETATM 21 O LIG 1 3.371 -3.470 -2.383 1.00 0.00 O

HETATM 22 H LIG 1 5.204 -2.581 -2.280 1.00 0.00 H

HETATM 23 C LIG 1 3.371 -3.470 -3.783 1.00 0.00 C

HETATM 24 C LIG 1 2.003 -3.470 -4.267 1.00 0.00 C

HETATM 25 H LIG 1 3.884 -2.581 -4.146 1.00 0.00 H

HETATM 26 H LIG 1 3.884 -4.359 -4.146 1.00 0.00 H

HETATM 27 H LIG 1 2.003 -3.470 -5.356 1.00 0.00 H

HETATM 28 H LIG 1 1.490 -4.359 -3.904 1.00 0.00 H

HETATM 29 O LIG 1 1.343 -2.327 -3.800 1.00 0.00 O

HETATM 30 C LIG 1 0.024 -2.327 -4.267 1.00 0.00 C

HETATM 31 C LIG 1 -0.660 -1.143 -3.783 1.00 0.00 C

HETATM 32 H LIG 1 0.024 -2.327 -5.356 1.00 0.00 H

HETATM 33 H LIG 1 -0.490 -3.216 -3.904 1.00 0.00 H

HETATM 34 H LIG 1 -1.687 -1.143 -4.146 1.00 0.00 H

HETATM 35 O LIG 1 -0.660 -1.143 -2.383 1.00 0.00 O

HETATM 36 H LIG 1 -0.147 -0.254 -4.146 1.00 0.00 H

HETATM 37 C LIG 1 -1.320 0.000 -1.917 1.00 0.00 C

HETATM 38 C LIG 1 -1.320 0.000 -0.467 1.00 0.00 C

HETATM 39 H LIG 1 -0.807 0.889 -2.280 1.00 0.00 H

HETATM 40 H LIG 1 -2.347 0.000 -2.280 1.00 0.00 H

HETATM 41 H LIG 1 -1.833 0.889 -0.104 1.00 0.00 H

HETATM 42 H LIG 1 -1.833 -0.889 -0.104 1.00 0.00 H

CONECT 1 38 2

CONECT 2 1 5 4 3

CONECT 2

CONECT 3 2 7 8 6

CONECT 3

CONECT 4 2

CONECT 5 2

CONECT 6 3

CONECT 7 9 3

CONECT 8 3

CONECT 9 10 7 11 12

CONECT 9

CONECT 10 15 13 14 9

CONECT 10

CONECT 11 9

CONECT 12 9

CONECT 13 10

CONECT 14 10

CONECT 15 16 10

CONECT 16 17 18 19 15

CONECT 16

CONECT 17 21 22 20 16

CONECT 17

CONECT 18 16

CONECT 19 16

CONECT 20 17

CONECT 21 23 17

CONECT 22 17

CONECT 23 24 26 25 21

CONECT 23

CONECT 24 27 28 29 23

CONECT 24

CONECT 25 23

CONECT 26 23

CONECT 27 24

CONECT 28 24

CONECT 29 24 30

CONECT 30 32 33 29 31

CONECT 30

CONECT 31 30 36 34 35

CONECT 31

CONECT 32 30

CONECT 33 30

CONECT 34 31

CONECT 35 31 37

CONECT 36 31

CONECT 37 35 39 40 38

CONECT 37

CONECT 38 37 41 42 1

CONECT 38

CONECT 39 37

CONECT 40 37

CONECT 41 38

CONECT 42 38

MASTER 0 0 0 0 0 0 0 0 42 0 42 0

END

Now my query is whether this pdb format i can directly used for pdb2gmx or
i have to change the "LIG" temr to OPLS force field term. If you can guide
here then the problem will be sorted out.



warm regards

SMA


On Sat, Aug 17, 2013 at 8:33 PM, Justin Lemkul  wrote:

>
>
> On 8/17/13 10:58 AM, Musharaf Ali wrote:
>
>> Thank You Justin
>> But you mean to say that even XYZ coordinates like below format
>> (18-crown-6) can be directly used in Gromacs.
>>
>>
> I don't know.  I seem to recall some discussion about .xyz files some time
> ago, but I forget the outcome.  My point was that most new users think that
> .gro files are absolutely required, which is not true.  Numerous file
> formats are accepted.  Check the manual and Gromacs website.  You may need
> to convert to another format, but it doesn't necessarily have to be .gro.
>
> -Justin
>
>  O 0.00 0.00 0.00
>>
>> C 0.00 0.00 1.40
>>
>> C 1.367075 0.00 1.883328
>>
>> H -0.513360 0.889165 1.763000
>>
>> H -0.513360 -0.889165 1.763000
>>
>> H 1.367079 0.00 2.972328
>>
>> O 2.027040 -1.143095 1.416659
>>
>> H 1.880433 0.889165 1.520326
>>
>> C 3.346974 -1.143095 1.883320
>>
>> C 4.030509 -2.327015 1.399984
>>
>> H 3.860332 -0.253930 1.520318
>>
>> H 3.346978 -1.143095 2.972320
>>
>> H 5.057229 -2.327015 1.762981
>>
>> H 3.517151 -3.216180 1.762986
>>
>> O 4.030503 -2.327015 -0.16
>>
>> C 4.690468 -3.470110 -0.466685
>>
>> C 4.690462 -3.470110 -1.916685
>>
>> H 5.717188 -3.470110 -0.103689
>>
>> H 4.177110 -4.359275 -0.103683
>>
>> H 5.203820 -4.359275 -2.279687
>>
>> O 3.370528 -3.470110 -2.383346
>>
>> H 5.203820 -2.580946 -2.279687
>>
>> C 3.370522 -3.470110 -3.783346
>>
>> C 2.003447 -3.470110 -4.266674
>>
>> H 3.883880 -2.

Re: [gmx-users] Lennard jones energy

2013-08-17 Thread Justin Lemkul 



On 8/17/13 4:22 PM, chinnu657 wrote:

Hi all,

Can someone please guide me on how I can use g_energy to print Lennard Jones
energy?



http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy

-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] Lennard jones energy

2013-08-17 Thread chinnu657 
Hi all,

Can someone please guide me on how I can use g_energy to print Lennard Jones
energy?

Thank you so much in advance.

Chinnu



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Re: [gmx-users] generation of gro file

2013-08-17 Thread Justin Lemkul 



On 8/17/13 10:58 AM, Musharaf Ali wrote:

Thank You Justin
But you mean to say that even XYZ coordinates like below format
(18-crown-6) can be directly used in Gromacs.



I don't know.  I seem to recall some discussion about .xyz files some time ago, 
but I forget the outcome.  My point was that most new users think that .gro 
files are absolutely required, which is not true.  Numerous file formats are 
accepted.  Check the manual and Gromacs website.  You may need to convert to 
another format, but it doesn't necessarily have to be .gro.


-Justin


O 0.00 0.00 0.00

C 0.00 0.00 1.40

C 1.367075 0.00 1.883328

H -0.513360 0.889165 1.763000

H -0.513360 -0.889165 1.763000

H 1.367079 0.00 2.972328

O 2.027040 -1.143095 1.416659

H 1.880433 0.889165 1.520326

C 3.346974 -1.143095 1.883320

C 4.030509 -2.327015 1.399984

H 3.860332 -0.253930 1.520318

H 3.346978 -1.143095 2.972320

H 5.057229 -2.327015 1.762981

H 3.517151 -3.216180 1.762986

O 4.030503 -2.327015 -0.16

C 4.690468 -3.470110 -0.466685

C 4.690462 -3.470110 -1.916685

H 5.717188 -3.470110 -0.103689

H 4.177110 -4.359275 -0.103683

H 5.203820 -4.359275 -2.279687

O 3.370528 -3.470110 -2.383346

H 5.203820 -2.580946 -2.279687

C 3.370522 -3.470110 -3.783346

C 2.003447 -3.470110 -4.266674

H 3.883880 -2.580946 -4.146348

H 3.883880 -4.359275 -4.146348

H 2.003443 -3.470110 -5.355674

H 1.490089 -4.359275 -3.903672

O 1.343483 -2.327015 -3.85

C 0.023548 -2.327015 -4.27

C -0.659986 -1.143095 -3.783331

H 0.023544 -2.327015 -5.355667

H -0.489810 -3.216180 -3.903665

H -1.686707 -1.143095 -4.146327

O -0.659981 -1.143095 -2.383331

H -0.146628 -0.253930 -4.146333

C -1.319945 0.00 -1.916662

C -1.319940 0.00 -0.42

H -0.806587 0.889165 -2.279664

H -2.34 0.00 -2.279658

H -1.833298 0.889165 -0.103660

H -1.833298 -0.889165 -0.103660


On Sat, Aug 17, 2013 at 3:53 PM, Justin Lemkul  wrote:




On 8/16/13 10:50 PM, Musharaf Ali wrote:


Hi
could somebody help how to generate grow file from xyz coordinates
specially for crown ether type molecules.



The specifications of the .gro format are described here:

http://manual.gromacs.org/**online/gro.html

Note that there is no requirement to use .gro files in Gromacs.  Most
formats will be recognized.


  Here the xyz coordinates are attached for 18-crown-6. Thank in advance.




FYI the mailing list does not accept attachments.

-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

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

==**
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 posting!
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--
==

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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Re: [gmx-users] generation of gro file

2013-08-17 Thread Musharaf Ali 
Thank You Justin
But you mean to say that even XYZ coordinates like below format
(18-crown-6) can be directly used in Gromacs.

O 0.00 0.00 0.00

C 0.00 0.00 1.40

C 1.367075 0.00 1.883328

H -0.513360 0.889165 1.763000

H -0.513360 -0.889165 1.763000

H 1.367079 0.00 2.972328

O 2.027040 -1.143095 1.416659

H 1.880433 0.889165 1.520326

C 3.346974 -1.143095 1.883320

C 4.030509 -2.327015 1.399984

H 3.860332 -0.253930 1.520318

H 3.346978 -1.143095 2.972320

H 5.057229 -2.327015 1.762981

H 3.517151 -3.216180 1.762986

O 4.030503 -2.327015 -0.16

C 4.690468 -3.470110 -0.466685

C 4.690462 -3.470110 -1.916685

H 5.717188 -3.470110 -0.103689

H 4.177110 -4.359275 -0.103683

H 5.203820 -4.359275 -2.279687

O 3.370528 -3.470110 -2.383346

H 5.203820 -2.580946 -2.279687

C 3.370522 -3.470110 -3.783346

C 2.003447 -3.470110 -4.266674

H 3.883880 -2.580946 -4.146348

H 3.883880 -4.359275 -4.146348

H 2.003443 -3.470110 -5.355674

H 1.490089 -4.359275 -3.903672

O 1.343483 -2.327015 -3.85

C 0.023548 -2.327015 -4.27

C -0.659986 -1.143095 -3.783331

H 0.023544 -2.327015 -5.355667

H -0.489810 -3.216180 -3.903665

H -1.686707 -1.143095 -4.146327

O -0.659981 -1.143095 -2.383331

H -0.146628 -0.253930 -4.146333

C -1.319945 0.00 -1.916662

C -1.319940 0.00 -0.42

H -0.806587 0.889165 -2.279664

H -2.34 0.00 -2.279658

H -1.833298 0.889165 -0.103660

H -1.833298 -0.889165 -0.103660


On Sat, Aug 17, 2013 at 3:53 PM, Justin Lemkul  wrote:

>
>
> On 8/16/13 10:50 PM, Musharaf Ali wrote:
>
>> Hi
>> could somebody help how to generate grow file from xyz coordinates
>> specially for crown ether type molecules.
>>
>
> The specifications of the .gro format are described here:
>
> http://manual.gromacs.org/**online/gro.html
>
> Note that there is no requirement to use .gro files in Gromacs.  Most
> formats will be recognized.
>
>
>  Here the xyz coordinates are attached for 18-crown-6. Thank in advance.
>>
>
> FYI the mailing list does not accept attachments.
>
> -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
>
> jalemkul@outerbanks.umaryland.**edu  |
> (410) 706-7441
>
> ==**
> --
> 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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[gmx-users] Problem in Gyrate analysis

2013-08-17 Thread Sainitin Donakonda 
Hello,

I performed 20ns MD simulations on Protein-Ligand Complex. Now i tried to
analysis this complex using g_gyrate.

Used following command

g_gyrate -s MD_first10.tpr -f File.xtc -n index.ndx -o ligand.xvg

I Choose Ligand group but it gives this following error..

*** glibc detected *** g_gyrate: munmap_chunk(): invalid pointer:
0x00b34140 ***
=== Backtrace: =
/lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fdbb9e84b96]
/usr/lib/libgmx.so.6(done_graph+0x35)[0x7fdbb96f25d5]
/usr/lib/libgmx.so.6(gmx_rmpbc_done+0x36)[0x7fdbb96aa436]
/usr/lib/libgmxana.so.6(gmx_gyrate+0xd0c)[0x7fdbba25000c]
g_gyrate(main+0x9)[0x400629]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fdbb9e2776d]
g_gyrate[0x400659]
=== Memory map: 
0040-00401000 r-xp  08:02 939978
/usr/bin/g_gyrate
0060-00601000 r--p  08:02 939978
/usr/bin/g_gyrate
00601000-00602000 rw-p 1000 08:02 939978
/usr/bin/g_gyrate
00b05000-00c5f000 rw-p  00:00 0
 [heap]
7fdbb7d56000-7fdbb7d6b000 r-xp  08:02 2354732
 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fdbb7d6b000-7fdbb7f6a000 ---p 00015000 08:02 2354732
 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fdbb7f6a000-7fdbb7f6b000 r--p 00014000 08:02 2354732
 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fdbb7f6b000-7fdbb7f6c000 rw-p 00015000 08:02 2354732
 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fdbb7f6c000-7fdbb80b rw-p  00:00 0
7fdbb80b1000-7fdbb8153000 rw-p  00:00 0
7fdbb818c000-7fdbb8193000 rw-p  00:00 0
7fdbb81f4000-7fdbb85a3000 rw-p  00:00 0
7fdbb85a3000-7fdbb867c000 rw-p  00:00 0
7fdbb867c000-7fdbb8692000 r-xp  08:02 2354831
 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fdbb8692000-7fdbb8891000 ---p 00016000 08:02 2354831
 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fdbb8891000-7fdbb8892000 r--p 00015000 08:02 2354831
 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fdbb8892000-7fdbb8893000 rw-p 00016000 08:02 2354831
 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fdbb8893000-7fdbb8895000 r-xp  08:02 2354860
 /lib/x86_64-linux-gnu/libdl-2.15.so
7fdbb8895000-7fdbb8a95000 ---p 2000 08:02 2354860
 /lib/x86_64-linux-gnu/libdl-2.15.so
7fdbb8a95000-7fdbb8a96000 r--p 2000 08:02 2354860
 /lib/x86_64-linux-gnu/libdl-2.15.so
7fdbb8a96000-7fdbb8a97000 rw-p 3000 08:02 2354860
 /lib/x86_64-linux-gnu/libdl-2.15.so
7fdbb8a97000-7fdbb8be8000 r-xp  08:02 1048574
 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
7fdbb8be8000-7fdbb8de8000 ---p 00151000 08:02 1048574
 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
7fdbb8de8000-7fdbb8df r--p 00151000 08:02 1048574
 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
7fdbb8df-7fdbb8df2000 rw-p 00159000 08:02 1048574
 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
7fdbb8df2000-7fdbb8df3000 rw-p  00:00 0
7fdbb8df3000-7fdbb8f57000 r-xp  08:02 1053298
 /usr/lib/libfftw3f.so.3.3.0
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Re: [gmx-users] generation of gro file

2013-08-17 Thread Justin Lemkul 



On 8/16/13 10:50 PM, Musharaf Ali wrote:

Hi
could somebody help how to generate grow file from xyz coordinates
specially for crown ether type molecules.


The specifications of the .gro format are described here:

http://manual.gromacs.org/online/gro.html

Note that there is no requirement to use .gro files in Gromacs.  Most formats 
will be recognized.



Here the xyz coordinates are attached for 18-crown-6. Thank in advance.


FYI the mailing list does not accept attachments.

-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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Re: [gmx-users] Regarding TCoupling and position restraints

2013-08-17 Thread Justin Lemkul 



On 8/17/13 12:10 AM, HANNIBAL LECTER wrote:

Thanks. Is there any way to position restraint a part of the system while
keeping all bonds flexible?



Sure.  Apply position restraints as normal and set "constraints = none" in the 
.mdp file.  This will affect your choice of dt, though, and SETTLE is still 
applied to water molecules.


-Justin



On Fri, Aug 16, 2013 at 5:24 PM, Justin Lemkul  wrote:




On 8/16/13 5:09 PM, HANNIBAL LECTER wrote:


Hi,
I am trying to simulate nanotube (1156) with protein and water and I am
using Tcoupl = system using sd integrator in gromacs.

Since I am position restraining the nanotube, I would expect that the
restrained CNT degrees of freedom are accounted for while calculating the
system temperatures using g_traj. However, for a ref-t = 300K the system
temperature is reported to be ~292K. As a control, I performed simulations
with
Tcoupl=CNT Protein SOL and in that case the temperatures from g_energy are
reported thus CNT~157K Protein~296K and Solvent ~300K. It clearly shows
that the CNT constrained dof are not accounted for correctly. Is that the
case or am I missing something?



Constraints are restraints are different.  If you are using constraints on
any bonds in your system, the value from g_traj is wrong and you have to
manually correct for it.

-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

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

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--
==

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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