subject:"\[gmx\-users\] RMSF problem"

Re: [gmx-users] RMSF problem

2017-05-12 Thread Mark Abraham

Also, knowing the group you selected in the mdp for writing the xtc file is
key to understanding why what you get might not match what you are trying
to do...

Mark

On Fri, May 12, 2017 at 1:51 PM Justin Lemkul  wrote:

>
>
> On 5/11/17 1:43 PM, Franco Henrique wrote:
> > Dear Justin Lemkul,
> >
> > Thank’s for prompt reply.
> >
> > My protein has 198 aminoacides (PDB: 2GOJ;
> http://www.rcsb.org/pdb/explore.do?structureId=2GOJ). After RMSF command
> (gmx rmsf -f .xtc -s .tpr -o .xvg -res), the output has only 103
> aminoacides as visualized by Grace software. I am running gromacs 5.1.2 in
> ubuntu.
> >
> > Any inquiries are more than welcome.
> >
>
> Your full screen output and an upload of the output file (to a file-sharing
> service, as the list does not accept attachments) would be helpful.
> There's no
> logical reason for gmx rmsf to randomly ignore residues.  Did you
> simulate/analyze the whole dimer structure, or just one chain?
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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Re: [gmx-users] RMSF problem

2017-05-12 Thread Justin Lemkul




On 5/11/17 1:43 PM, Franco Henrique wrote:

Dear Justin Lemkul,

Thank’s for prompt reply.

My protein has 198 aminoacides (PDB: 2GOJ; 
http://www.rcsb.org/pdb/explore.do?structureId=2GOJ). After RMSF command (gmx 
rmsf -f .xtc -s .tpr -o .xvg -res), the output has only 103 aminoacides as 
visualized by Grace software. I am running gromacs 5.1.2 in ubuntu.

Any inquiries are more than welcome.



Your full screen output and an upload of the output file (to a file-sharing 
service, as the list does not accept attachments) would be helpful.  There's no 
logical reason for gmx rmsf to randomly ignore residues.  Did you 
simulate/analyze the whole dimer structure, or just one chain?


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] RMSF problem

2017-05-11 Thread Franco Henrique

Dear Justin Lemkul,

Thank’s for prompt reply.

My protein has 198 aminoacides (PDB: 2GOJ; 
http://www.rcsb.org/pdb/explore.do?structureId=2GOJ). After RMSF command (gmx 
rmsf -f .xtc -s .tpr -o .xvg -res), the output has only 103 aminoacides as 
visualized by Grace software. I am running gromacs 5.1.2 in ubuntu.

Any inquiries are more than welcome.

Best regards,
Franco Henrique.
--
Doutor em Biotecnologia
Professor Assistente B 
Departamento de Saúde - DSAU
Universidade Estadual de Feira de Santana - UEFS
Avenida Transnordestina s/n, bairro Novo Horizonte CEP 44.036-900 - Feira de 
Santana – BA

Em 11 de mai de 2017, à(s) 14:28, Justin Lemkul  escreveu:

On 5/11/17 1:21 PM, Franco Henrique wrote:
> Dear,
> 
> I am have problem with RMSF data, because after I apply this command-line: 
> gmx rmsf -f xxx.xtc -s yyy.tpr -o zzz.xvg -res, the .xvg file has not all 
> residues of protein. If possible, I would like to know a tip to solve this 
> problem.
> 

How many residues do you have, and how many did the program output?  No GROMACS 
program will magically get rid of anything; it will analyze what you tell it 
to, so without more information about what you did, which group you chose, etc. 
it's hard to suggest anything.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] RMSF problem

2017-05-11 Thread Justin Lemkul




On 5/11/17 1:21 PM, Franco Henrique wrote:

Dear,

I am have problem with RMSF data, because after I apply this command-line: gmx 
rmsf -f xxx.xtc -s yyy.tpr -o zzz.xvg -res, the .xvg file has not all residues 
of protein. If possible, I would like to know a tip to solve this problem.



How many residues do you have, and how many did the program output?  No GROMACS 
program will magically get rid of anything; it will analyze what you tell it to, 
so without more information about what you did, which group you chose, etc. it's 
hard to suggest anything.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
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[gmx-users] RMSF problem

2017-05-11 Thread Franco Henrique

Dear,

I am have problem with RMSF data, because after I apply this command-line: gmx 
rmsf -f xxx.xtc -s yyy.tpr -o zzz.xvg -res, the .xvg file has not all residues 
of protein. If possible, I would like to know a tip to solve this problem.

Best regards,
Franco Henrique.
--
Doutor em Biotecnologia
Professor Assistente B 
Departamento de Saúde - DSAU
Universidade Estadual de Feira de Santana - UEFS
Avenida Transnordestina s/n, bairro Novo Horizonte CEP 44.036-900 - Feira de 
Santana – BA

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Re: [gmx-users] RMSF problem

Re: [gmx-users] RMSF problem

Re: [gmx-users] RMSF problem

Re: [gmx-users] RMSF problem

[gmx-users] RMSF problem

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