Re: [gmx-users] uninstall gromacs 5.0

[sun]

I am sorry for so many e-mails but check this link: 
http://installion.co.uk/ubuntu/vivid/universe/g/gromacs/uninstall/index.html

Sent from my iPhone

> On 23-May-2016, at 9:49 pm, Mark Abraham  wrote:
> 
> Hi,
> 
> sun, that is not the name of any apt-supported GROMACS package that I know
> of...
> 
> Mark
> 
>> On Mon, May 23, 2016 at 6:17 PM sun  wrote:
>> 
>> sudo apt-get uninstall Gromacs-5.0
>> 
>> 
>> 
>> Sent from my iPhone
>> 
 On 23-May-2016, at 6:51 pm, Anurag Dobhal <
>>> anurag.dob...@nano-medicine.co.in> wrote:
>>> 
>>> Dear Users:
>>> 
>>> I want to uninstall gromacs 5.0 and replace it with gromacs 5.1.
>>> The link provided in the gromacs website (Removing a GROMACS
>> installation)
>>> does not give any solution with the same.
>>> 
>>> how can i uninstall gromacs 5.0 ??
>>> 
>>> 
>>> Thanks in advance.
>>> 
>>> Anurag Dobhal
>>> 
>>> --
>>> 
>>> 
>>> *DISCLAIMER:*
>>> 
>>> *This communication is intended only for the person or entity to which it
>>> is addressed and may contain confidential and / or privileged material.
>> Any
>>> review, retransmission, dissemination or other use is prohibited. If you
>>> have received this in error, please contact the sender and delete this
>>> material from your computer. Any comments or statements made herein do
>> not
>>> necessarily reflect those of Nanomedicine Research Group.  Before opening
>>> the email or accessing any attachments, please check and scan for virus.*
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
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Re: [gmx-users] uninstall gromacs 5.0

[sun]

Running make uninstall also works

Sent from my iPhone

> On 23-May-2016, at 9:49 pm, Mark Abraham  wrote:
> 
> Hi,
> 
> sun, that is not the name of any apt-supported GROMACS package that I know
> of...
> 
> Mark
> 
>> On Mon, May 23, 2016 at 6:17 PM sun  wrote:
>> 
>> sudo apt-get uninstall Gromacs-5.0
>> 
>> 
>> 
>> Sent from my iPhone
>> 
 On 23-May-2016, at 6:51 pm, Anurag Dobhal <
>>> anurag.dob...@nano-medicine.co.in> wrote:
>>> 
>>> Dear Users:
>>> 
>>> I want to uninstall gromacs 5.0 and replace it with gromacs 5.1.
>>> The link provided in the gromacs website (Removing a GROMACS
>> installation)
>>> does not give any solution with the same.
>>> 
>>> how can i uninstall gromacs 5.0 ??
>>> 
>>> 
>>> Thanks in advance.
>>> 
>>> Anurag Dobhal
>>> 
>>> --
>>> 
>>> 
>>> *DISCLAIMER:*
>>> 
>>> *This communication is intended only for the person or entity to which it
>>> is addressed and may contain confidential and / or privileged material.
>> Any
>>> review, retransmission, dissemination or other use is prohibited. If you
>>> have received this in error, please contact the sender and delete this
>>> material from your computer. Any comments or statements made herein do
>> not
>>> necessarily reflect those of Nanomedicine Research Group.  Before opening
>>> the email or accessing any attachments, please check and scan for virus.*
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] uninstall gromacs 5.0

[sun]

I am so sorry Mark
It sudo apt-get remove Gromacs :) 
I used this in Ubuntu. Also, for Gromacs and its dependencies:
sudo apt-get remove --auto-remove gromacs
I hope this works


Sent from my iPhone

> On 23-May-2016, at 9:49 pm, Mark Abraham  wrote:
> 
> Hi,
> 
> sun, that is not the name of any apt-supported GROMACS package that I know
> of...
> 
> Mark
> 
>> On Mon, May 23, 2016 at 6:17 PM sun  wrote:
>> 
>> sudo apt-get uninstall Gromacs-5.0
>> 
>> 
>> 
>> Sent from my iPhone
>> 
 On 23-May-2016, at 6:51 pm, Anurag Dobhal <
>>> anurag.dob...@nano-medicine.co.in> wrote:
>>> 
>>> Dear Users:
>>> 
>>> I want to uninstall gromacs 5.0 and replace it with gromacs 5.1.
>>> The link provided in the gromacs website (Removing a GROMACS
>> installation)
>>> does not give any solution with the same.
>>> 
>>> how can i uninstall gromacs 5.0 ??
>>> 
>>> 
>>> Thanks in advance.
>>> 
>>> Anurag Dobhal
>>> 
>>> --
>>> 
>>> 
>>> *DISCLAIMER:*
>>> 
>>> *This communication is intended only for the person or entity to which it
>>> is addressed and may contain confidential and / or privileged material.
>> Any
>>> review, retransmission, dissemination or other use is prohibited. If you
>>> have received this in error, please contact the sender and delete this
>>> material from your computer. Any comments or statements made herein do
>> not
>>> necessarily reflect those of Nanomedicine Research Group.  Before opening
>>> the email or accessing any attachments, please check and scan for virus.*
>>> --
>>> 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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>> send a mail to gmx-users-requ...@gromacs.org.
>> --
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Re: [gmx-users] ERROR in Membrane-protein simulation

[Mark Abraham]

Hi,

You didn't finish writing this email, but I'll bet lunch that you didn't
update the top file like the tutorial suggested :-)

Mark

On Mon, 23 May 2016 17:48 BIJENDRA KHADKA  wrote:

> Hello Everyone,
> I received an error (shown below) while trying to run "Adding ion" step
> during
> Protein-membrane simulation. Any advice or suggestions will be greatly
> appreciated.
>
> The steps utilized proior to "Adding Ions" are mention below:
>
> > pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water
> spc
> Topology file updated (as indicated in tutorial)
> > editconf -f dppc128.pdb -o dppc128.gro
>
> > grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
>
> > cat KALP-15_processed.gro dppc128_whole.gro > system.gro
>
> > editconf -f system.gro -o system_box.gro -box 6.41840 6.44350 10.59650
>
> > solvate -cp  system_box.gro -cs spc216.gro -o system_box_sol.gro
>
> >
>
> --
>
> *Bijen*
> --
> Gromacs Users mailing list
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Re: [gmx-users] uninstall gromacs 5.0

[sun]

sudo apt-get uninstall Gromacs-5.0 



Sent from my iPhone

> On 23-May-2016, at 6:51 pm, Anurag Dobhal  
> wrote:
> 
> Dear Users:
> 
> I want to uninstall gromacs 5.0 and replace it with gromacs 5.1.
> The link provided in the gromacs website (Removing a GROMACS installation)
> does not give any solution with the same.
> 
> how can i uninstall gromacs 5.0 ??
> 
> 
> Thanks in advance.
> 
> Anurag Dobhal
> 
> -- 
> 
> 
> *DISCLAIMER:*
> 
> *This communication is intended only for the person or entity to which it 
> is addressed and may contain confidential and / or privileged material. Any 
> review, retransmission, dissemination or other use is prohibited. If you 
> have received this in error, please contact the sender and delete this 
> material from your computer. Any comments or statements made herein do not 
> necessarily reflect those of Nanomedicine Research Group.  Before opening 
> the email or accessing any attachments, please check and scan for virus.*
> -- 
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> 
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Re: [gmx-users] uninstall gromacs 5.0

[Mark Abraham]

Hi,

sun, that is not the name of any apt-supported GROMACS package that I know
of...

Mark

On Mon, May 23, 2016 at 6:17 PM sun  wrote:

> sudo apt-get uninstall Gromacs-5.0
>
>
>
> Sent from my iPhone
>
> > On 23-May-2016, at 6:51 pm, Anurag Dobhal <
> anurag.dob...@nano-medicine.co.in> wrote:
> >
> > Dear Users:
> >
> > I want to uninstall gromacs 5.0 and replace it with gromacs 5.1.
> > The link provided in the gromacs website (Removing a GROMACS
> installation)
> > does not give any solution with the same.
> >
> > how can i uninstall gromacs 5.0 ??
> >
> >
> > Thanks in advance.
> >
> > Anurag Dobhal
> >
> > --
> >
> >
> > *DISCLAIMER:*
> >
> > *This communication is intended only for the person or entity to which it
> > is addressed and may contain confidential and / or privileged material.
> Any
> > review, retransmission, dissemination or other use is prohibited. If you
> > have received this in error, please contact the sender and delete this
> > material from your computer. Any comments or statements made herein do
> not
> > necessarily reflect those of Nanomedicine Research Group.  Before opening
> > the email or accessing any attachments, please check and scan for virus.*
> > --
> > 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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> > 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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[gmx-users] ERROR in Membrane-protein simulation

[BIJENDRA KHADKA]

Hello Everyone,
I received an error (shown below) while trying to run "Adding ion" step
during
Protein-membrane simulation. Any advice or suggestions will be greatly
appreciated.

The steps utilized proior to "Adding Ions" are mention below:

> pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water
spc
Topology file updated (as indicated in tutorial)
> editconf -f dppc128.pdb -o dppc128.gro

> grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr

> cat KALP-15_processed.gro dppc128_whole.gro > system.gro

> editconf -f system.gro -o system_box.gro -box 6.41840 6.44350 10.59650

> solvate -cp  system_box.gro -cs spc216.gro -o system_box_sol.gro

>

-- 

*Bijen*
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Re: [gmx-users] uninstall gromacs 5.0

[Mark Abraham]

Hi,

You can run "make uninstall" from your build directory (as root), but I
don't know how good a job that really does. If you've installed to the
default location of /usr/local/gromacs then you can also just delete that
(as root). Or just don't bother uninstalling (you might want it later!) and
instead install another version wherever you want, and use your choice of
which GMXRC to source into your shell's environment to control how you work.

Mark

On Mon, May 23, 2016 at 3:21 PM Anurag Dobhal <
anurag.dob...@nano-medicine.co.in> wrote:

> Dear Users:
>
> I want to uninstall gromacs 5.0 and replace it with gromacs 5.1.
> The link provided in the gromacs website (Removing a GROMACS installation)
> does not give any solution with the same.
>
> how can i uninstall gromacs 5.0 ??
>
>
> Thanks in advance.
>
> Anurag Dobhal
>
> --
>
>
> *DISCLAIMER:*
>
> *This communication is intended only for the person or entity to which it
> is addressed and may contain confidential and / or privileged material. Any
> review, retransmission, dissemination or other use is prohibited. If you
> have received this in error, please contact the sender and delete this
> material from your computer. Any comments or statements made herein do not
> necessarily reflect those of Nanomedicine Research Group.  Before opening
> the email or accessing any attachments, please check and scan for virus.*
> --
> 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
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] uninstall gromacs 5.0

[Anurag Dobhal]

Dear Users:

I want to uninstall gromacs 5.0 and replace it with gromacs 5.1.
The link provided in the gromacs website (Removing a GROMACS installation)
does not give any solution with the same.

how can i uninstall gromacs 5.0 ??


Thanks in advance.

Anurag Dobhal

-- 


*DISCLAIMER:*

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is addressed and may contain confidential and / or privileged material. Any 
review, retransmission, dissemination or other use is prohibited. If you 
have received this in error, please contact the sender and delete this 
material from your computer. Any comments or statements made herein do not 
necessarily reflect those of Nanomedicine Research Group.  Before opening 
the email or accessing any attachments, please check and scan for virus.*
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Re: [gmx-users] find out tpx version of tpr

[Sabine Reisser]

Thanks, that works.

The log file has only the mdrun version. Only if executable and tpr file 
version differ, there's a note. Same with gmx dump and check.


Cheers
Sabine

On 05/23/2016 11:39 AM, Tsjerk Wassenaar wrote:

Hey :)

If you just have the .tpr and you don't want to use Gromacs' tools, you can
use python:

python -c 'import struct; print
"".join(struct.unpack(100*"c",open("YOUR-TPR-HERE").read(100)))'

(Python 2, mind you).

Cheers,

Tsjerk

On Mon, May 23, 2016 at 11:33 AM, Mark Abraham 
wrote:


Hi,

Mdrun reports it to the log file, or likely gmx dump and gmx check also do
so.

Mark

On Mon, 23 May 2016 11:12 Sabine Reisser  wrote:


Hello,

how can I find out the tpx version of a tpr file?

Cheers
Sabine
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Re: [gmx-users] find out tpx version of tpr

[Tsjerk Wassenaar]

Hey :)

If you just have the .tpr and you don't want to use Gromacs' tools, you can
use python:

python -c 'import struct; print
"".join(struct.unpack(100*"c",open("YOUR-TPR-HERE").read(100)))'

(Python 2, mind you).

Cheers,

Tsjerk

On Mon, May 23, 2016 at 11:33 AM, Mark Abraham 
wrote:

> Hi,
>
> Mdrun reports it to the log file, or likely gmx dump and gmx check also do
> so.
>
> Mark
>
> On Mon, 23 May 2016 11:12 Sabine Reisser  wrote:
>
> > Hello,
> >
> > how can I find out the tpx version of a tpr file?
> >
> > Cheers
> > Sabine
> > --
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> >
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Re: [gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr

[Mark Abraham]

Hi,

Justin suggested confirming with gmx check. Since we know the file is
large, find out what your file system is, or try another machine.

Mark

On Mon, 23 May 2016 10:50 Antara mazumdar  wrote:

> Dear Mark,
>
>I checked the file size , MD.trr is 3.2 Terabytes. It is a million atom
> system. What further could be done?
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
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Re: [gmx-users] find out tpx version of tpr

[Mark Abraham]

Hi,

Mdrun reports it to the log file, or likely gmx dump and gmx check also do
so.

Mark

On Mon, 23 May 2016 11:12 Sabine Reisser  wrote:

> Hello,
>
> how can I find out the tpx version of a tpr file?
>
> Cheers
> Sabine
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[gmx-users] Generating topology for a HEM protein with CHARMM27

[zeineb SI CHAIB]

I'm looking to generate the topology of a HEM protein , I choose CHARMM as a 
force field. At the begining, when I run pdb2gmx I had this error about missing 
hydrogen's:

WARNING:
atom HA is missing in residue HEM 473 in the pdb file

You
might need to add atom HA to the hydrogen database of building block
HEME

in
the file aminoacids.hdb (see the manual)






WARNING:
atom HB is missing in residue HEM 473 in the pdb file

You
might need to add atom HB to the hydrogen database of building block
HEME

in
the file aminoacids.hdb (see the manual)









---
Program
pdb2gmx, VERSION 4.6.5
Source
code file: /build/buildd/gromacs-4.6.5/src/kernel/pdb2top.c, line:
1588



Fatal
error:
There
were 30 missing atoms in molecule Other2, if you want to use this
incomplete topology anyhow, use the option -missing
For
more information and tips for troubleshooting, please check the
GROMACS
website
at http://www.gromacs.org/Documentation/Errors
---
After a research, I found what was missing: I made a copy of aminoacids.hdb 
(Charmm27.ff folder) in my working directory and I edited this file: 
I added the following Lines: 











HEME 16 

1
  1   HA
 CHA C1A C4D
1
  1   HB
 CHB C4A C1B
1
  1   HC
 CHC C1C C4B
1
  1   HD
 CHD C1D C4C
3
  4   HMA
CMA C3A C2A
2
  6   HAA
CAA C2A
CBA
2
  6   HBA
CBA CAA
CGA
3
  4   HMB
CMB C2B C1B
1
  1   HAB
CAB C3B CBB
2
  3   HBB
CBB CAB C3B
3
  4   HMC
CMC C2C C1C
1
  1   HAC
CAC CBC C3C
2
  3   HBC
CBC CAC C3C
3
  4   HMD
CMD C2D C1D
2
  6   HAD
CAD C2D CBD
2
  6   HBD
CBD CAD CGD



I fixed the problem of missing hydrogens but I'm having another type of error:

Special Atom Distance matrix:
  HEM360  HEM360
CAB2CAC3
  HEM360CAC3   0.796
  HEM360FE43   0.557   0.557

---
Program gmx pdb2gmx, VERSION 5.1.2
Source code file: 
/home/francois/Bureau/Zineb/gromacs-5.1.2/src/gromacs/gmxpreprocess/resall.c, 
line: 645

Fatal error:
Residue 'HEM' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I added an entry in residuetype.dat (HEM  Protein), after making a copy in 
my working directory but it didn't fix the problem. I verified each file and 
they seem OK, I can't find where is the problem!!! Any help please!!!

Kind regards. 

Zeineb. 

  
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[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr

[Antara mazumdar]

Dear Mark,

   I checked the file size , MD.trr is 3.2 Terabytes. It is a million atom
system. What further could be done?
Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
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Re: [gmx-users] g_cluster analysis

[Tsjerk Wassenaar]

Hi Sapna,

How should we know how many clusters you should have?

A cutoff of 0.2 is quite tight, and will give many clusters. Whether that's
what you want/need or whether that's meaningful/helpful for your goals is
something you should consider. We don't know what you're trying or doing.

Cheers,

Tsjerk

On Mon, May 23, 2016 at 9:03 AM, SAPNA BORAH  wrote:

> Dear all,
>
> I am trying to use g_cluster protocol to get representative snapshots of
> the simulations. I have concatenated 9 set of simulations and run g_cluster
> for the same. The result shows a total of 198 clusters.
>
> Is this correct?
>
> Following is the command I have used:
>
> g_cluster -s models.gro -f concatenated.xtc -dm rmsd-matrix.xpm -o
> clusters.xpm -sz cluster_size.xvg -clid cluster-id-over-time.xvg -cl
> all_clusters.pdb -cutoff 0.2 -method gromos
>
> Thanks in advance.
>
> Regards,
> Sapna.
>
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
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[gmx-users] g_cluster analysis

[SAPNA BORAH]

Dear all,

I am trying to use g_cluster protocol to get representative snapshots of
the simulations. I have concatenated 9 set of simulations and run g_cluster
for the same. The result shows a total of 198 clusters.

Is this correct?

Following is the command I have used:

g_cluster -s models.gro -f concatenated.xtc -dm rmsd-matrix.xpm -o
clusters.xpm -sz cluster_size.xvg -clid cluster-id-over-time.xvg -cl
all_clusters.pdb -cutoff 0.2 -method gromos

Thanks in advance.

Regards,
Sapna.

Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India
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