Re: [gmx-users] Simulation protocol for Protein-DNA-complex

[Peter C. Lai]

If there is tutorial for a system like yours it would probably have to be
(re)constructed from someone's publication. Multi-molecule systems shouldn't
be much different from your "typical" receptor-ligand system; if there isn't
a covalent bond between your dna and protein then life is even easier:
parameterize each as independent molecules, strip out everything after
the molecule topology, then use a system-wide .top that #includes 
each molecule's .itp file.

The integrator = steep scheme should not be sending whole molecules across 
the universe.

Does your anomaly happen even if you turn off periodic boundary 
conditions (pbc=no)?  (I noticed for my own system that sometimes doing a 
minimization in vacuum of a ligand by itself with pbc turned on causes the 
coordinates for an adjacent cell to be output, which when merged with the 
coordinates of the receptor causes the ligand to be located far away from
the receptor. I figured it's easier to just turn off pbc for vacuum
minimizations instead of trying to unwrap the pbc consistently.
Note that you can't use PME without PBC, you will need to use a pure
cutoff scheme (which will may generate a warning about artifacts but it's
EM so it's fine).


On 2012-05-25 04:01:52PM +0200, Matthias Ernst wrote:
> Hi,
> 
> I have a question regarding simulation of a protein-DNA-complex where 
> the protein encloses the DNA double helix. I did not find a tutorial for 
> a system of three rather big molecules like these, that's why I ask. If 
> there is such, I would appreciate a hint.
> 
> I want to start with a crystal structure from PDB. When I do the steps 
> in J. Lemkuls tutorial "Lysozyme in water", first thing would be an 
> energy minimization in vacuo. Unfortunately, doing this I end up with 
> the two strands of the DNA double helix being far away from the protein 
> and seperated from each other. Can this result from clashes and 
> therefore high energy in the system that allows the DNA strands to move 
> "through" the protein or how else can this happen? And how can I prevent 
> this?
> 
> I mean, usually the protocol is:
> - minimize system in vacuo
> - add solvent and ions
> - minimize again
> - add thermostat and barostat
> - simulate
> Obviously, I cannot follow this if the first step already does not work. 
> When I tried to skip in-vacuo-minimization and to minimize the system in 
> solvent, it ended up bei either reaching machine precision without the 
> maximum force being small enough or in the simulation, the atom were 
> moving to fast. Would it be a good idea to use position restraints for 
> the minimizations? If yes, for which part, in which order and in which 
> steps?
> 
> Thank you for your help,
> Matthias
> -- 
> 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/Search before 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

-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

-- 
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/Search before 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

[gmx-users] PubChem Online Compound Search and Download

[Nancy]

Hi All,

I have been using the PubChem database to search for uncharged small
molecules.  However, even after specifying zero charge, PubChem still
outputs compounds containing amino groups (-NH2) and carboxylic acids
(-COOH); since I am interested in physiological pH, these compounds would
actually be charged.

Is there some way to exclude molecules containing these functional groups?
I've noticed that there is an option on PubChem to include only certain
atoms, but the search times out at 2 minutes if I try this.  I'd like to
exclude halogens and aldehydes as well, can this be specified?  Finally,
after searching for numerous compounds, how could all of them be downloaded
into an organized compound library?

If there is another online compound database besides PubChem that can be
easily searched and has the same or better functionality, I'd greatly
appreciate any info about it.

Thanks,
Nancy
-- 
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/Search before 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

Re: [gmx-users] Bonds between New residues and Terminals

[Justin A. Lemkul]

On 5/25/12 5:43 PM, Steven Neumann wrote:

Dear Gmx Users,

My surface is made of 4 types of residues created on my own. They are placed
within they vdwradii away from each other. I want to keep the surface rigid and
allow it to move into only one direction (freezgrps, freezdim). Each residue is
made of one atom. The best option would be to create bonds between or apply
distnce restraints e.g. using cutoff of 1nm.

How can I create bonds between them? Shall I specify in my aminoacids.rtp the
possibilities of each of them to create bonds with any 3 others? Then to add
proper lines to specbond.dat?
I want two of them to create extra bond with my protein terminals. How to do
this using bonds? Or would you suggest distance restraints?



The nature of the model depends on how you want to treat them.  Distance 
restraints are harmonic potentials that can be set up with arbitrary 
flexibility.  Bonds can be harmonic or rigid, depending on the use of 
constraints.  The manner that makes the most sense for what you hope to achieve 
should prevail.


As for creating the topology, you can only use pdb2gmx to create a linear 
sequence of bonded residues.  Thus, you can't specify all possible bonds within 
the .rtp file; the majority of the work comes in creating suitable entries in 
specbond.dat.  There are a number of discussions in the list archive about doing 
so, usually in the context of silica-type species.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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/Search before 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

[gmx-users] Bonds between New residues and Terminals

[Steven Neumann]

Dear Gmx Users,

My surface is made of 4 types of residues created on my own. They are
placed within they vdwradii away from each other. I want to keep the
surface rigid and allow it to move into only one direction (freezgrps,
freezdim). Each residue is made of one atom. The best option would be to
create bonds between or apply distnce restraints e.g. using cutoff of 1nm.

How can I create bonds between them? Shall I specify in my aminoacids.rtp
the possibilities of each of them to create bonds with any 3 others? Then
to add proper lines to specbond.dat?
I want two of them to create extra bond with my protein terminals. How to
do this using bonds? Or would you suggest distance restraints?

Thank you in advance,

Steven
-- 
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/Search before 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

Re: [gmx-users] unknown cmap torsion between atoms

[Justin A. Lemkul]

On 5/25/12 5:04 PM, Steven Neumann wrote:



On Fri, May 25, 2012 at 2:34 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



On 5/25/12 5:52 AM, Steven Neumann wrote:

Dear Gmx Users,

My system is made of 3 proteins. As I want to use distance restraints
dynamics
between atoms belonging to each of them I have to produce topoloy with 
one
moleculetype. I used pdb2gmx -chainsep interactive (I used merge: yes).

Then when I process to grompp the error: "unknown cmap torsion between 
atoms
..."

These atoms belong to the last residue of the chain A and to the first
residue
of Chain B. How to get rid of this? Please, help.


http://redmine.gromacs.org/__issues/885 


Either apply Mark's patch posted there or download the latest
release-4-5-patches branch via git.

-Justin


Thanks! I need to talk to the administrator as the Gromacs I am using is on the
cluster. Would you suggest to install GMX 4.5.5 first and then apply the patch?



It is generally best to work with the latest version unless you have some reason 
(like scientific continuity) to use an old version, especially when applying 
patches and bug fixes.  You can always install within your own home directory if 
you don't want to wait on an admin to install a (technically) non-standard 
Gromacs version system-wide.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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/Search before 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

Re: [gmx-users] Re: One molculetype for 3 proteins

[Steven Neumann]

Thanks Francesca. There is no bond between them. I merged topologies and
the grompp error comes from the gmx bug posted by Mark.
http://redmine.gromacs.org/issues/885
Thanks for this link Justin!

Steven

On Fri, May 25, 2012 at 5:47 PM, Francesca wrote:

> if you create a bond you need to have angle, tortion etc...
> Maybe when you processed pb2gmx it create a bond between the 799 and 801.
> Francesca
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/One-molculetype-for-3-proteins-tp4997727p4997773.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> 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/Search before 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
>
-- 
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/Search before 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

Re: [gmx-users] unknown cmap torsion between atoms

[Steven Neumann]

On Fri, May 25, 2012 at 2:34 PM, Justin A. Lemkul  wrote:

>
>
> On 5/25/12 5:52 AM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> My system is made of 3 proteins. As I want to use distance restraints
>> dynamics
>> between atoms belonging to each of them I have to produce topoloy with one
>> moleculetype. I used pdb2gmx -chainsep interactive (I used merge: yes).
>>
>> Then when I process to grompp the error: "unknown cmap torsion between
>> atoms
>> ..."
>>
>> These atoms belong to the last residue of the chain A and to the first
>> residue
>> of Chain B. How to get rid of this? Please, help.
>>
>>
> http://redmine.gromacs.org/**issues/885
>
> Either apply Mark's patch posted there or download the latest
> release-4-5-patches branch via git.
>
> -Justin
>
>
Thanks! I need to talk to the administrator as the Gromacs I am using is on
the cluster. Would you suggest to install GMX 4.5.5 first and then apply
the patch?

Steven



> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
> --
> 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
>
-- 
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/Search before 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

Re: [gmx-users] unknown cmap torsion between atoms

[Justin A. Lemkul]

On 5/25/12 5:52 AM, Steven Neumann wrote:

Dear Gmx Users,

My system is made of 3 proteins. As I want to use distance restraints dynamics
between atoms belonging to each of them I have to produce topoloy with one
moleculetype. I used pdb2gmx -chainsep interactive (I used merge: yes).

Then when I process to grompp the error: "unknown cmap torsion between atoms
..."

These atoms belong to the last residue of the chain A and to the first residue
of Chain B. How to get rid of this? Please, help.



http://redmine.gromacs.org/issues/885

Either apply Mark's patch posted there or download the latest 
release-4-5-patches branch via git.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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/Search before 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

Re: [gmx-users] ptn ptn interaction

[Justin A. Lemkul]

On 5/25/12 3:19 AM, rethina malliga wrote:


On 5/24/12 7:43 AM, rethina malliga wrote:
 > Hi,
 >
 > I tried protein protein simulation in gromacs.
 >
 > I prepared one ptn and kept seperately with its .top, .itp, .gro files.
 >
 > Then I prepared another protein and I build the complex of pasting the
.gro file
 > of first processed protein in the .gro file of second processed ptn.
 >
 > In the topol.top  of second protein I included the molecule type at the
bottom
 > and inserted
 >;Include ligand topology
 >#include "posre.itp"
 >

Be careful about name clashes here - the first protein (by default) will 
have a
file named "posre.itp" that will be applied to it.  If you use the same 
name for
different files, you'll probably get other errors.  I find it useful to call
everything based on specific names, like "posre_proteinA.itp" or something
similar.

 > And i run succeccfully the newbox generation, solvent adding commands.
 >
 > But with the ions adding command it shows fatal error that the atoms in
 > topol.top and solv.gro is different.
 >
 > `Fatal error:
 > number of coordinates in coordinate file (solv.gro, 231262)
 >   does not match topology (topol.top, 237548)
 >
 > on analysing the difference between two files i come to know that it is
taking
 > the atoms of first protein for the second protein though i named first 
and
 > second proteins different.
 >

After you added the second protein, did you correctly update the [molecules]
section of the topology?

 > I changed the residue information in .gro of first file to 1LIG and 
change
 > everything regarding second molecules name as 1LIG
 >

Unless your protein residues are all called LIG, then this is not 
appropriate.

 > and after retrying the ions adding command it says no such molecule type
found.
 >
 > `Fatal error:
 > No such moleculetype 1LIG
 > For more information and tips for troubleshooting, please check the 
GROMACS
 > website at http://www.gromacs.org/Documentation/Errors
 >

This comes from incorrect naming.  Updating [molecules] correctly with the 
name
of your second protein [moleculetype] will solve it.  Make sure you make 
changes
to both the coordinate file and topology at all steps - they should always
match.



Hi Justin,

I tried again with correct namings. If I leave the original name for second
protein molecule type (Protein_chain_A) unaltered  it shows difference in atoms
of topol.top and solv.gro. If I alter the molecule type, where ever its instance
appears it shows molecule type not found.

Thanks in advance



Please don't reply to the entire digest message; it becomes hopelessly 
confusing.  Your approach of leaving the original names in place is the best way 
to proceed.  As for the error that arises about coordinates and topology not 
matching, consult this document:


http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

The solution is always better bookkeeping.  You may wish to start over, prior to 
solvation, and have tools like genbox and genion do all the bookkeeping for you 
by invoking the -p flag with each.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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/Search before 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

Re: [gmx-users] Simulation protocol for Protein-DNA-complex

[Justin A. Lemkul]

On 5/25/12 10:01 AM, Matthias Ernst wrote:

Hi,

I have a question regarding simulation of a protein-DNA-complex where the
protein encloses the DNA double helix. I did not find a tutorial for a system of
three rather big molecules like these, that's why I ask. If there is such, I
would appreciate a hint.



In principle, it is no different from the lysozyme tutorial cited below.  The 
workflow starts with pdb2gmx, which can handle all the molecules in the system 
(protein and water) and then you solvate, add ions, and simulate.  There's not 
much very special in this case.



I want to start with a crystal structure from PDB. When I do the steps in J.
Lemkuls tutorial "Lysozyme in water", first thing would be an energy
minimization in vacuo. Unfortunately, doing this I end up with the two strands
of the DNA double helix being far away from the protein and seperated from each
other. Can this result from clashes and therefore high energy in the system that
allows the DNA strands to move "through" the protein or how else can this
happen? And how can I prevent this?



I suspect this is more a result of periodicity than anything else.  Depending on 
how bad the initial geometry is, this in vacuo minimization may not be 
completely necessary.  You can test an in vacuo minimization by using "pbc = no" 
and/or setting an unreasonably large box with:


editconf -f conf.gro -o hugebox.gro -c -d 10

In this instance, with the protein/DNA complex centered in a huge box, there's 
no way you'll get breaks across periodic boundaries during EM.



I mean, usually the protocol is:
- minimize system in vacuo
- add solvent and ions
- minimize again
- add thermostat and barostat
- simulate
Obviously, I cannot follow this if the first step already does not work. When I
tried to skip in-vacuo-minimization and to minimize the system in solvent, it
ended up bei either reaching machine precision without the maximum force being
small enough or in the simulation, the atom were moving to fast. Would it be a
good idea to use position restraints for the minimizations? If yes, for which
part, in which order and in which steps?



Position restraints for EM will likely make the outcome worse, as any necessary 
tweaks that may need to happen during EM will be disfavored due to the applied 
restraints.  I never use position restraints during EM for similar systems. 
Perhaps one can think of instances where some restraints might be useful, but I 
don't think this is one of them.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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/Search before 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

[gmx-users] Re: FCC lattice of argon

[Dr. Vitaly V. Chaban]

Ahmed -

This is *YOUR* research, not mine. I believe I have given you enough
hints to succeed.


Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA



On Fri, May 25, 2012 at 12:51 PM, ahmed sta  wrote:
> Can you help me please
>
>
> Thanks for all
>
> 
> De : Dr. Vitaly V. Chaban 
> À : ahmed sta 
> Cc : gmx-users@gromacs.org
> Envoyé le : Vendredi 25 mai 2012 17h33
> Objet : Re: Re : Re : Re : Gromacs
>
> Sure, possible.
>
> But if you want to type the coordinates for FCC lattice using 500
> atoms by hand, that's indeed cool.
>
>
>
> On Fri, May 25, 2012 at 11:31 AM, ahmed sta  wrote:
>> I thought that it is possible to use text editor in order to fix the
>> geometry, isn't it?
>>
>>
>> 
>> De : Dr. Vitaly V. Chaban 
>> À : ahmed sta 
>> Cc : gmx-users@gromacs.org
>> Envoyé le : Vendredi 25 mai 2012 18h15
>> Objet : Re: Re : Re : Gromacs
>>
>> Writing your program has nothing to do with gromacs. If you do not
>> have experience in programming by far, it may be faster to use the
>> second route. But of you still want to generate a program yourself, I
>> am delighted to direct your attention to the PYTHON, python.org,
>> programming language.
>>
>> I am aware of some commercial software like MedeA and (perhaps?)
>> Materials Studio, capable to generate molecular configurations of
>> various symmetries. Maybe, someone in the gromacs mailing list can
>> suggest a free alternative as well.
>>
>>
>>
>> On Fri, May 25, 2012 at 11:05 AM, ahmed sta  wrote:
>>> Well i see
>>>
>>> I think that writing my own program would be better and more accurate
>>> How should i proceed ?
>>> it is my first use of Gromacs and i do not know how to do
>>>
>>> Regards
>>>
>>> 
>>> De : Dr. Vitaly V. Chaban 
>>> À : ahmed sta 
>>> Cc : gmx-users@gromacs.org
>>> Envoyé le : Vendredi 25 mai 2012 17h58
>>> Objet : Re: Re : Gromacs
>>>
>>> If you want a solid system, where atoms are arranged as in FCC, this
>>> is another talk.
>>>
>>> There two way to achieve your goal. Either --
>>>
>>> 1) you write a simple program which places argon atoms as in FCC.
>>>
>>> OR
>>>
>>> 2) you try to freeze my system into your system using simulated
>>> annealing implemented in gromacs. Provided that argon is a pretty
>>> simple system, this should not take too much time. At least, I can say
>>> that our students get it (216 atoms) freezed during one laboratory
>>> work.
>>>
>>> BTW, there is no guarantee that the freezing point of the classical
>>> argon model is perfectly reproduced. My guess is based on the fact
>>> that the density of the liquid phase (in the NPT ensemble) is not
>>> ideal.
>>>
>>>
>>> Dr. Vitaly V. Chaban, 430 Hutchison Hall
>>> Dept. Chemistry, University of Rochester
>>> 120 Trustee Road, Rochester, NY 14627-0216
>>> THE UNITED STATES OF AMERICA
>>>
>>>
>>>
>>> On Fri, May 25, 2012 at 10:44 AM, ahmed sta 
>>> wrote:
 Sorry. My aim is to model FCC Argon (not liquid state) and i am trying
 to
 define that geometry
 Can you help me please?

 Regards

 
 De : Dr. Vitaly V. Chaban 
 À : ahmed sta 
 Cc : gmx-users@gromacs.org
 Envoyé le : Vendredi 25 mai 2012 17h36
 Objet : Re: Gromacs

 Dear Ahmed -

 I do not understand how you imagine "FCC geometry" in the liquid state
 of matter.

 If you want to just resize my system, use the standard "genbox"
 utility and then re-equilibrate at the desired temperature and density
 (if you want to fix density, of course).


 Dr. Vitaly V. Chaban, 430 Hutchison Hall
 Dept. Chemistry, University of Rochester
 120 Trustee Road, Rochester, NY 14627-0216
 THE UNITED STATES OF AMERICA



 On Fri, May 25, 2012 at 10:30 AM, ahmed sta 
 wrote:
>     Dear Vitaly
>
>
> I am an engineer student and i am now trying to use Gromacs
> I found your Argon molecule defined topology created in May 2009
> I want to ask you how to define my own geometry on Gromacs
> In fact i am trying to define liquid Argon system with a density
> equilibrated at 90K. My system should have a FCC geometry and
> containing
> for
> example 500 atoms
>
>
> I really need your help
>
> Best regards
>
>
>
>
> Ahmed Sta
> Ensta Paristech engineering school
> ahmedsta6...@yahoo.fr


>>>
>>>
>>
>>
>
>
>
> --
> Dr. Vitaly V. Chaban, 430 Hutchison Hall
> Dept. Chemistry, University of Rochester
> 120 Trustee Road, Rochester, NY 14627-0216
> THE UNITED STATES OF AMERICA
>
--
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/Search before posting!
Please don't post (u

[gmx-users] Re: One molculetype for 3 proteins

[Francesca]

if you create a bond you need to have angle, tortion etc...
Maybe when you processed pb2gmx it create a bond between the 799 and 801.
Francesca

--
View this message in context: 
http://gromacs.5086.n6.nabble.com/One-molculetype-for-3-proteins-tp4997727p4997773.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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/Search before 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

Re: [gmx-users] Re: One molculetype for 3 proteins

[Tsjerk Wassenaar]

Hi Steven,

There will be three dihedrals spanning a break. Make sure to remove all of
them. Of course pdb2gmx shouldn't just connect the chain ends... Maybe you
can file it as a bug.

Cheers,

Tsjerk

On May 25, 2012 3:11 PM, "Steven Neumann"  wrote:

Yes, it works (-chainsep interactive: merge = yes ) but when you process to
grompp there is an error:

Unknown cmap torsion between atoms 6002 6004 6006 6017 6021

pdb2gmx takes the cmap for the atoms e.g. last two residues of chain A with
first three residues of chain B. Removing these lines does not solve the
problem. Any suggestions appreciated!



On Fri, May 25, 2012 at 9:57 AM, Steven Neumann wrote:

>
>
> > On Thu, May 24, 2012 at 10:04 PM, Francesca <
> francesca.stanzi...@unina.it> wrote: >> >> I checked ...
>
> Yes, it works (-chainsep interactive: merge = no ) but when you process to
> grompp there is an error:
>
> Unknown cmap torsion between atoms 6002 6004 6006 6017 6021
>
> pdb2gmx takes the cmap for the atoms e.g. last two residues of chain A
> with first three residues of chain B. Does removing this lines will be
> reasonable or some torsions wont be taken into account?
>
> Steven
>
> >> >> >> -- >> View this message in context:
> http://gromacs.5086.n6.nabble.com/One-molculetype-for-3...
>
>

--
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/Search before 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
-- 
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/Search before 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

Re: [gmx-users] sudden jumps in RMSD etc.

[mu xiaojia]

probably means your trajectory is not continuous enough. I saw the same
thing when I try to "fit" an ensemble trajectory, which each frame is not
from the previous one. Or if your first frame in your trajectory is not
"good looking(or having good rmsd to your target structure)", fit option
cannot fit the rest to such starting structure.

On Thu, Jan 19, 2012 at 4:32 PM, Mark Abraham wrote:

> On 20/01/2012 7:55 AM, Yun Shi wrote:
>
>> Hi all,
>>
>> I am doing duplicate MD simulations with a protein-ligand system.
>>
>> After processing one trajectory by trjconv with the optioin -pbc nojump,
>> I still find abrupt jumps (on the scale of nm) in RMSDs and COM distances.
>>
>> Then I tried -pbc mol -ur compact, which did not work. And then -fit
>> progressive on protein atoms, which again did not completely eliminate
>> those jumps in protein atom RMSDs.
>>
>> I wonder if I have not used the right option?
>>
>
> There's a suggested workflow here http://www.gromacs.org/**
> Documentation/Terminology/**Periodic_Boundary_Conditionswhich
>  you can adapt to your needs.
>
> Mark
> --
> 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
>
-- 
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/Search before 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

Re: [gmx-users] unknown cmap torsion between atoms

[Steven Neumann]

On Fri, May 25, 2012 at 4:18 PM, Mark Abraham wrote:

> On 25/05/2012 7:52 PM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> My system is made of 3 proteins. As I want to use distance restraints
>> dynamics between atoms belonging to each of them I have to produce topoloy
>> with one moleculetype. I used pdb2gmx -chainsep interactive (I used merge:
>> yes).
>>
>> Then when I process to grompp the error: "unknown cmap torsion between
>> atoms  ..."
>>
>> These atoms belong to the last residue of the chain A and to the first
>> residue of Chain B. How to get rid of this? Please, help.
>>
>
> What version is this? I seem to recall fixing this bug at some stage.
>
> Mark
>

Its 4.5.4 - but the atoms belonging to these residues of one chain are
created on my own. I added them to residuetypes.dat and to my
aminoacids.rtp. They are nonbonded group of residues forming a planar
surface. When I remove their CMAP the same error occurs between next two
proteins which are formed of existing bonded residues. Do you have an idea
how to deal with this?

Steven


> --
> 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
>
-- 
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/Search before 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

[gmx-users] Re: Re : Re : Gromacs

[Dr. Vitaly V. Chaban]

Writing your program has nothing to do with gromacs. If you do not
have experience in programming by far, it may be faster to use the
second route. But of you still want to generate a program yourself, I
am delighted to direct your attention to the PYTHON, python.org,
programming language.

I am aware of some commercial software like MedeA and (perhaps?)
Materials Studio, capable to generate molecular configurations of
various symmetries. Maybe, someone in the gromacs mailing list can
suggest a free alternative as well.



On Fri, May 25, 2012 at 11:05 AM, ahmed sta  wrote:
> Well i see
>
> I think that writing my own program would be better and more accurate
> How should i proceed ?
> it is my first use of Gromacs and i do not know how to do
>
> Regards
>
> 
> De : Dr. Vitaly V. Chaban 
> À : ahmed sta 
> Cc : gmx-users@gromacs.org
> Envoyé le : Vendredi 25 mai 2012 17h58
> Objet : Re: Re : Gromacs
>
> If you want a solid system, where atoms are arranged as in FCC, this
> is another talk.
>
> There two way to achieve your goal. Either --
>
> 1) you write a simple program which places argon atoms as in FCC.
>
> OR
>
> 2) you try to freeze my system into your system using simulated
> annealing implemented in gromacs. Provided that argon is a pretty
> simple system, this should not take too much time. At least, I can say
> that our students get it (216 atoms) freezed during one laboratory
> work.
>
> BTW, there is no guarantee that the freezing point of the classical
> argon model is perfectly reproduced. My guess is based on the fact
> that the density of the liquid phase (in the NPT ensemble) is not
> ideal.
>
>
> Dr. Vitaly V. Chaban, 430 Hutchison Hall
> Dept. Chemistry, University of Rochester
> 120 Trustee Road, Rochester, NY 14627-0216
> THE UNITED STATES OF AMERICA
>
>
>
> On Fri, May 25, 2012 at 10:44 AM, ahmed sta  wrote:
>> Sorry. My aim is to model FCC Argon (not liquid state) and i am trying to
>> define that geometry
>> Can you help me please?
>>
>> Regards
>>
>> 
>> De : Dr. Vitaly V. Chaban 
>> À : ahmed sta 
>> Cc : gmx-users@gromacs.org
>> Envoyé le : Vendredi 25 mai 2012 17h36
>> Objet : Re: Gromacs
>>
>> Dear Ahmed -
>>
>> I do not understand how you imagine "FCC geometry" in the liquid state
>> of matter.
>>
>> If you want to just resize my system, use the standard "genbox"
>> utility and then re-equilibrate at the desired temperature and density
>> (if you want to fix density, of course).
>>
>>
>> Dr. Vitaly V. Chaban, 430 Hutchison Hall
>> Dept. Chemistry, University of Rochester
>> 120 Trustee Road, Rochester, NY 14627-0216
>> THE UNITED STATES OF AMERICA
>>
>>
>>
>> On Fri, May 25, 2012 at 10:30 AM, ahmed sta  wrote:
>>>     Dear Vitaly
>>>
>>>
>>> I am an engineer student and i am now trying to use Gromacs
>>> I found your Argon molecule defined topology created in May 2009
>>> I want to ask you how to define my own geometry on Gromacs
>>> In fact i am trying to define liquid Argon system with a density
>>> equilibrated at 90K. My system should have a FCC geometry and containing
>>> for
>>> example 500 atoms
>>>
>>>
>>> I really need your help
>>>
>>> Best regards
>>>
>>>
>>>
>>>
>>> Ahmed Sta
>>> Ensta Paristech engineering school
>>> ahmedsta6...@yahoo.fr
>>
>>
>
>
--
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/Search before 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

[gmx-users] "Mutating" type BAR calculations

[jrustad]

Dear All

Although the tutorials on FE calculations are all excellent and useful, they
all appear to involve turning a molecule on or off.  As I understand the
manual, it is also possible to change one atom into another, i.e. lambda=1
means 100% state A (and 0% state B) and lambda=0 means 100% state B (and 0%
state A)

I would assume in this case that "couple-lambda0" and "couple-lambda1" are
both set to "vdw-q", in other words, the VDW and coulomb interactions are
both "on" for each state?

I say this because I am having strange behavior where the VDW terms for
state A and state B appear to be added together at lambda=1.  In other
words, the VDW terms for state A were not turned off at lambda=1.  This
looks like a bug to me, however, I am too new to GROMACS to be comfortable
coming to such a conclusion.

I should also mention that I am using user-defined tables for the
short-ranged interactions.  From the manual, I cannot tell for sure whether
such tables are definitely supported in BAR (or, I suppose, in Free Energy
calculations in general)

I would be grateful for any insight into this problem

Jim Rustad

--
View this message in context: 
http://gromacs.5086.n6.nabble.com/Mutating-type-BAR-calculations-tp4997768.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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/Search before 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

Re: [gmx-users] Re: One molculetype for 3 proteins

[Steven Neumann]

On Fri, May 25, 2012 at 4:15 PM, Francesca wrote:

> can you write the atoms 6002 6004 6006 6017 6021 and all informations in
> your
> topology file about these atoms??
>
> Francesca
>

Sure:

>From the begining:

Unknown cmap torsion between atoms 799 801 804 811 813


; residue 399 NON rtp NON  q +0.6
   799  C399NON  C799   0.62 12.011   ;
qtot -81.13
; residue 400 POL rtp POL  q -0.5
   800  N400POL  N800  -0.47 14.007   ;
qtot -81.6
; residue   1 SER rtp SER  q  0.0
   801NH2  1SER  N801  -0.96 14.007   ;
qtot -82.56
   802  H  1SERHT1802   0.34  1.008   ;
qtot -82.22
   803  H  1SERHT2803   0.34  1.008   ;
qtot -81.88
   804CT1  1SER CA804   0.19 12.011   ;
qtot -81.69
   805 HB  1SER HA805   0.09  1.008   ;
qtot -81.6
   806CT2  1SER CB806   0.05 12.011   ;
qtot -81.55
   807 HA  1SERHB1807   0.09  1.008   ;
qtot -81.46
   808 HA  1SERHB2808   0.09  1.008   ;
qtot -81.37
   809OH1  1SER OG809  -0.66 15.999   ;
qtot -82.03
   810  H  1SERHG1810   0.43  1.008   ;
qtot -81.6
   811  C  1SER  C811   0.51 12.011   ;
qtot -81.09
   812  O  1SER  O812  -0.51 15.999   ;
qtot -81.6
; residue   2 GLY rtp GLY  q  0.0
   813NH1  2GLY  N813  -0.47 14.007   ;
qtot -82.07
   814  H  2GLY HN814   0.31  1.008   ;
qtot -81.76
   815CT2  2GLY CA815  -0.02 12.011   ;
qtot -81.78
   816 HB  2GLYHA1816   0.09  1.008   ;
qtot -81.69
   817 HB  2GLYHA2817   0.09  1.008   ;
qtot -81.6
   818  C  2GLY  C818   0.51 12.011   ;
qtot -81.09
   819  O  2GLY  O819  -0.51 15.999   ;
qtot -81.6

Where NON and POL are residues made on my own (residue = atom) which are in
the aminoacids.rtp. I also added them to the residuetypes.dat. They form a
planar surface (400 of them). Is it because there is no data of cmap on
those atoms?
Why do I do this? I want to use distance restrain of my protein terminal
with one of the atoms belonging to the "surface" made of those created
atoms to mimic the attached protein to the surface. Maybe its easier to
form a bond?

Steven




>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/One-molculetype-for-3-proteins-tp4997727p4997758.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> 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/Search before 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
>
-- 
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/Search before 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

[gmx-users] Re: Re : Gromacs

[Dr. Vitaly V. Chaban]

If you want a solid system, where atoms are arranged as in FCC, this
is another talk.

There two way to achieve your goal. Either --

1) you write a simple program which places argon atoms as in FCC.

OR

2) you try to freeze my system into your system using simulated
annealing implemented in gromacs. Provided that argon is a pretty
simple system, this should not take too much time. At least, I can say
that our students get it (216 atoms) freezed during one laboratory
work.

BTW, there is no guarantee that the freezing point of the classical
argon model is perfectly reproduced. My guess is based on the fact
that the density of the liquid phase (in the NPT ensemble) is not
ideal.


Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA



On Fri, May 25, 2012 at 10:44 AM, ahmed sta  wrote:
> Sorry. My aim is to model FCC Argon (not liquid state) and i am trying to
> define that geometry
> Can you help me please?
>
> Regards
>
> 
> De : Dr. Vitaly V. Chaban 
> À : ahmed sta 
> Cc : gmx-users@gromacs.org
> Envoyé le : Vendredi 25 mai 2012 17h36
> Objet : Re: Gromacs
>
> Dear Ahmed -
>
> I do not understand how you imagine "FCC geometry" in the liquid state
> of matter.
>
> If you want to just resize my system, use the standard "genbox"
> utility and then re-equilibrate at the desired temperature and density
> (if you want to fix density, of course).
>
>
> Dr. Vitaly V. Chaban, 430 Hutchison Hall
> Dept. Chemistry, University of Rochester
> 120 Trustee Road, Rochester, NY 14627-0216
> THE UNITED STATES OF AMERICA
>
>
>
> On Fri, May 25, 2012 at 10:30 AM, ahmed sta  wrote:
>>     Dear Vitaly
>>
>>
>> I am an engineer student and i am now trying to use Gromacs
>> I found your Argon molecule defined topology created in May 2009
>> I want to ask you how to define my own geometry on Gromacs
>> In fact i am trying to define liquid Argon system with a density
>> equilibrated at 90K. My system should have a FCC geometry and containing
>> for
>> example 500 atoms
>>
>>
>> I really need your help
>>
>> Best regards
>>
>>
>>
>>
>> Ahmed Sta
>> Ensta Paristech engineering school
>> ahmedsta6...@yahoo.fr
>
>
--
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/Search before 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

[gmx-users] nbnxn_hybrid_acc branch rewritten

[Szilárd Páll]

Hi,

Due to a mistake during commit cleanup we had to rewrite part of the
history of the nbnxn_hybrid_acc branch. As a consequence, pulling from
branches that track nbnxn_hybrid_acc will not work (it will result in
conflicts) and a forced update will be required:

$ git branch
nbnxn_hybrid_acc   # current branch is tracking nbnxn_hybrid_acc!
$ git remote update
[...]
$ git reset --hard origin/nbnxn_hybrid_acc

Sorry for the inconvenience!

Cheers,
--
Szilárd
--
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/Search before 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

[gmx-users] Re: Re : Re : Re : Gromacs

[Dr. Vitaly V. Chaban]

Sure, possible.

But if you want to type the coordinates for FCC lattice using 500
atoms by hand, that's indeed cool.



On Fri, May 25, 2012 at 11:31 AM, ahmed sta  wrote:
> I thought that it is possible to use text editor in order to fix the
> geometry, isn't it?
>
>
> 
> De : Dr. Vitaly V. Chaban 
> À : ahmed sta 
> Cc : gmx-users@gromacs.org
> Envoyé le : Vendredi 25 mai 2012 18h15
> Objet : Re: Re : Re : Gromacs
>
> Writing your program has nothing to do with gromacs. If you do not
> have experience in programming by far, it may be faster to use the
> second route. But of you still want to generate a program yourself, I
> am delighted to direct your attention to the PYTHON, python.org,
> programming language.
>
> I am aware of some commercial software like MedeA and (perhaps?)
> Materials Studio, capable to generate molecular configurations of
> various symmetries. Maybe, someone in the gromacs mailing list can
> suggest a free alternative as well.
>
>
>
> On Fri, May 25, 2012 at 11:05 AM, ahmed sta  wrote:
>> Well i see
>>
>> I think that writing my own program would be better and more accurate
>> How should i proceed ?
>> it is my first use of Gromacs and i do not know how to do
>>
>> Regards
>>
>> 
>> De : Dr. Vitaly V. Chaban 
>> À : ahmed sta 
>> Cc : gmx-users@gromacs.org
>> Envoyé le : Vendredi 25 mai 2012 17h58
>> Objet : Re: Re : Gromacs
>>
>> If you want a solid system, where atoms are arranged as in FCC, this
>> is another talk.
>>
>> There two way to achieve your goal. Either --
>>
>> 1) you write a simple program which places argon atoms as in FCC.
>>
>> OR
>>
>> 2) you try to freeze my system into your system using simulated
>> annealing implemented in gromacs. Provided that argon is a pretty
>> simple system, this should not take too much time. At least, I can say
>> that our students get it (216 atoms) freezed during one laboratory
>> work.
>>
>> BTW, there is no guarantee that the freezing point of the classical
>> argon model is perfectly reproduced. My guess is based on the fact
>> that the density of the liquid phase (in the NPT ensemble) is not
>> ideal.
>>
>>
>> Dr. Vitaly V. Chaban, 430 Hutchison Hall
>> Dept. Chemistry, University of Rochester
>> 120 Trustee Road, Rochester, NY 14627-0216
>> THE UNITED STATES OF AMERICA
>>
>>
>>
>> On Fri, May 25, 2012 at 10:44 AM, ahmed sta  wrote:
>>> Sorry. My aim is to model FCC Argon (not liquid state) and i am trying to
>>> define that geometry
>>> Can you help me please?
>>>
>>> Regards
>>>
>>> 
>>> De : Dr. Vitaly V. Chaban 
>>> À : ahmed sta 
>>> Cc : gmx-users@gromacs.org
>>> Envoyé le : Vendredi 25 mai 2012 17h36
>>> Objet : Re: Gromacs
>>>
>>> Dear Ahmed -
>>>
>>> I do not understand how you imagine "FCC geometry" in the liquid state
>>> of matter.
>>>
>>> If you want to just resize my system, use the standard "genbox"
>>> utility and then re-equilibrate at the desired temperature and density
>>> (if you want to fix density, of course).
>>>
>>>
>>> Dr. Vitaly V. Chaban, 430 Hutchison Hall
>>> Dept. Chemistry, University of Rochester
>>> 120 Trustee Road, Rochester, NY 14627-0216
>>> THE UNITED STATES OF AMERICA
>>>
>>>
>>>
>>> On Fri, May 25, 2012 at 10:30 AM, ahmed sta 
>>> wrote:
     Dear Vitaly


 I am an engineer student and i am now trying to use Gromacs
 I found your Argon molecule defined topology created in May 2009
 I want to ask you how to define my own geometry on Gromacs
 In fact i am trying to define liquid Argon system with a density
 equilibrated at 90K. My system should have a FCC geometry and containing
 for
 example 500 atoms


 I really need your help

 Best regards




 Ahmed Sta
 Ensta Paristech engineering school
 ahmedsta6...@yahoo.fr
>>>
>>>
>>
>>
>
>



-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA
--
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/Search before 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

[gmx-users] Re: Gromacs

[Dr. Vitaly V. Chaban]

Dear Ahmed -

I do not understand how you imagine "FCC geometry" in the liquid state
of matter.

If you want to just resize my system, use the standard "genbox"
utility and then re-equilibrate at the desired temperature and density
(if you want to fix density, of course).


Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA



On Fri, May 25, 2012 at 10:30 AM, ahmed sta  wrote:
>     Dear Vitaly
>
>
> I am an engineer student and i am now trying to use Gromacs
> I found your Argon molecule defined topology created in May 2009
> I want to ask you how to define my own geometry on Gromacs
> In fact i am trying to define liquid Argon system with a density
> equilibrated at 90K. My system should have a FCC geometry and containing for
> example 500 atoms
>
>
> I really need your help
>
> Best regards
>
>
>
>
> Ahmed Sta
> Ensta Paristech engineering school
> ahmedsta6...@yahoo.fr
--
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/Search before 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

Re: [gmx-users] unknown cmap torsion between atoms

[Mark Abraham]

On 25/05/2012 7:52 PM, Steven Neumann wrote:

Dear Gmx Users,

My system is made of 3 proteins. As I want to use distance restraints 
dynamics between atoms belonging to each of them I have to produce 
topoloy with one moleculetype. I used pdb2gmx -chainsep interactive (I 
used merge: yes).


Then when I process to grompp the error: "unknown cmap torsion between 
atoms  ..."


These atoms belong to the last residue of the chain A and to the first 
residue of Chain B. How to get rid of this? Please, help.


What version is this? I seem to recall fixing this bug at some stage.

Mark
--
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/Search before 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

[gmx-users] Re: Justin umbrella sampling tutorial......

[Thomas Schlesier]

I think all the answers to your question are in the tutorial. Probably 
read first the  lysozyme tutorial and then the umbrella tutorial again.


But here is a more general answer:

Normally you have two types of simulations:
preperation (which is also equilibration)
production
and the need of restraints depends on what you want to achive.

So if you want to calculate some equilibrium property of a protein in 
water you do first a preperation simulation to equilibrate the system 
(NVE, NVT or NPT - depending for what ensemble you want the property).
Normally during this you put position restraints to the protein 
backbone, so that the protein structure does not gets disturbed during 
the part where you equilibrate the water. but if your protein is fairly 
stable / rigid, you don't need these restraints.
Then you do the production simulation. Normally without restraints, 
since you want to know the property for a protein in equilibrium. But 
you could also do this with the same position restraints, in the extrem 
case, when you freeze the protein, you would get the property for a 
special protein geometry (the one to which ou restrain the coordinates).

-> So it really depends on what you want to do!!!

For the umbrella tutorial:
As far as i remember, Justin used the restrains for one of the chains 
(B), so to conserve the structure of said chain, because when one pull 
chain A away this would have an influence to the structure of chain B 
(they interact with each other).
BUT: one could also dismiss these restrains during the umbrella 
simulations, since it is expected the structure of chain B depends on 
the distance to chain A (since they interact).
You could also restrain only that part of chain B, which does not 
interact directly with chain A, to conserve a part of the structure of B 
(so you would be in the middle between the two extreme cases above).


In all three cases you get a different answer (like above for the 
equilibrium property). One could argue which is the better option, but i 
think all three have their right to exist, since the answer to this also 
depends on the initial question. Best would be to do all three cases, 
but mostly one does not have so much time. So one must stick to one.


Which leads to:
First think about your question.
Then think about how to answer it (think often there will be different 
possibilities / methods).

Then decide what to do...
Since the answer you get (may) depend on the method you use, you should 
justify your decission.


Hope this helps
greetings
thomas



Thank you Justin for these correct explanation
>  Its really clear my lot of queries..
>
>   For the tutorial, NPT is conducted with restraints on all protein heavy
>   atoms.  The production runs are conducted by restraining only one chain 
for
>   practical reasons.
>
>   These is my question ;
>
>  If we are doing NPT with restraints on all protein atom and production run by
>  conducted by restraining only one chain for protein...
>
>  means NPT and productin run mdp files should be different , Where these
>  information in mdp files???
>  It my request to you please tell me why these mdp files are almost same in
>  parameter ..
>
>  (Where you mentioned in mdp for npt to do restraints on all proteins heavy 
atoms
>  and for production md restraining only
>  one chain ..)
>

I don't understand what more I can say beyond what I already have.

-Justin


--
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/Search before 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

Re: [gmx-users] electrostatic component of the forces

[Mark Abraham]

On 25/05/2012 7:44 PM, Julian Mondon-Garrec wrote:

Hi all,

I am trying to get the electrostatic forces acting on each atom as a 
function of time. I have checked the list and all the suggestions are 
based on rerunning the simulation. Is there not an easy way to print 
these forces on the fly ?


You can print the whole force "on the fly" with nstfout, but you cannot 
decompose it.


If not, what is the cleanest way to remove bonded and vdw components 
from the forces ? One option could be to set all the unwanted 
interaction to zero in the topology file but I am wondering if there 
is a safer alternative.


The code permits such a "safe" alternative, by not setting 
GMX_FORCE_BONDED, but there is no way to access that setting from the 
command line. The best you can easily do is mdrun -rerun with parameters 
zeroed.


Mark
--
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/Search before 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

[gmx-users] Re: One molculetype for 3 proteins

[Francesca]

can you write the atoms 6002 6004 6006 6017 6021 and all informations in your
topology file about these atoms??

Francesca

--
View this message in context: 
http://gromacs.5086.n6.nabble.com/One-molculetype-for-3-proteins-tp4997727p4997758.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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/Search before 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

Re: [gmx-users] Regarding error

[Justin A. Lemkul]

On 5/25/12 1:23 AM, Seera Suryanarayana wrote:

Dear all gromacs users,

   While i am using the commond" pdb2gmx -f
4E82.pdb -o 4E82.gro -p 4E82.top".I am getting the following warnings and 
errors.



Warning: Residue EME21 in chain has different type (Other) from starting residue
ALA1 (Protein).
Warning: Residue ILE22 in chain has different type (Protein) from starting
residue ALA1 (Protein).
Warning: Residue SER23 in chain has different type (Protein) from starting
residue ALA1 (Protein).
Warning: Residue GLY24 in chain has different type (Protein) from starting
residue ALA1 (Protein).
Warning: Residue ARG25 in chain has different type (Protein) from starting
residue ALA1 (Protein).
More than 5 unidentified residues at end of chain - disabling further warnings.
Identified residue CYS20 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
 CYS3CYS5   CYS10   CYS20   CYS30
 SG18SG36SG75   SG144   SG228
 CYS5SG36   0.834
CYS10SG75   0.936   1.000
CYS20   SG144   0.833   0.203   0.935
CYS30   SG228   0.856   0.827   0.200   0.788
CYS31   SG234   0.202   0.860   0.783   0.820   0.734
Linking CYS-3 SG-18 and CYS-31 SG-234...
Linking CYS-5 SG-36 and CYS-20 SG-144...
Linking CYS-10 SG-75 and CYS-30 SG-228...
Start terminus ALA-1: NH3+
End terminus CYS-20: COO-

Fatal error:
Residue 'EME' not found in residue topology database.

Kindly tell me how to over come this error.



Whenever you encounter an error, your first source of information should be 
http://www.gromacs.org/Documentation/Errors.  This error, and most of the others 
you are likely to encounter, have been asked and answered hundreds (if not 
thousands) of times already.  For instance:


http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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/Search before 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

[gmx-users] Simulation protocol for Protein-DNA-complex

[Matthias Ernst]

Hi,

I have a question regarding simulation of a protein-DNA-complex where 
the protein encloses the DNA double helix. I did not find a tutorial for 
a system of three rather big molecules like these, that's why I ask. If 
there is such, I would appreciate a hint.


I want to start with a crystal structure from PDB. When I do the steps 
in J. Lemkuls tutorial "Lysozyme in water", first thing would be an 
energy minimization in vacuo. Unfortunately, doing this I end up with 
the two strands of the DNA double helix being far away from the protein 
and seperated from each other. Can this result from clashes and 
therefore high energy in the system that allows the DNA strands to move 
"through" the protein or how else can this happen? And how can I prevent 
this?


I mean, usually the protocol is:
- minimize system in vacuo
- add solvent and ions
- minimize again
- add thermostat and barostat
- simulate
Obviously, I cannot follow this if the first step already does not work. 
When I tried to skip in-vacuo-minimization and to minimize the system in 
solvent, it ended up bei either reaching machine precision without the 
maximum force being small enough or in the simulation, the atom were 
moving to fast. Would it be a good idea to use position restraints for 
the minimizations? If yes, for which part, in which order and in which 
steps?


Thank you for your help,
Matthias
--
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/Search before 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

[gmx-users] Problems of gmx4.5.5 on the E3-1230 V2 CPU (Ivy Bridge)

[??????]

Dear??every one!

We found some problems of run gmx4.5.5 in parallel on the E3-1230 V2 CPU (Ivy 
Bridge).
The compilers we used were ifort and icc (Version 12.0.3).
It only if the value of the option "-nt" > 2, the mdrun program crashed after 
hundreds MD steps.
And we also noticed that the same .tpr file could successfully run on both the 
i7-2600 and AMD platforms.

The typically error outputs are attached below. Thanks for any responses and 
suggestions.

Wade Lv


Error Outputs:
==
step 222: Water molecule starting at atom 3633 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 222: Water molecule starting at atom 3882 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

---
Program mdrun, VERSION 4.5.5
Source code file: pme.c, line: 538

Fatal error:
1 particles communicated to PME node 0 are more than 2/3 times the cut-off out 
of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
=-- 
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/Search before 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

Re: [gmx-users] Extraction of low-energy conformations

[Tsjerk Wassenaar]

Hi Andrej,

You can use trjconv with -drop and -dropunder. Check trjconv -h.

Cheers,

Tsjerk

On Fri, May 25, 2012 at 11:03 AM, Андрей Гончар  wrote:
> Hello.
> How to extract all low-energy conformations from MD-trajectory of protein?
>
> --
>
> Андрей Гончар
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before 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



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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/Search before 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

RE: [gmx-users] Regarding error

[Marzinek, Jan]

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Seera Suryanarayana [paluso...@gmail.com]
Sent: Friday, May 25, 2012 6:23 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Regarding error

Dear all gromacs users,

  While i am using the commond" pdb2gmx -f 
4E82.pdb -o 4E82.gro -p 4E82.top".I am getting the following warnings and 
errors.



Warning: Residue EME21 in chain has different type (Other) from starting 
residue ALA1 (Protein).
Warning: Residue ILE22 in chain has different type (Protein) from starting 
residue ALA1 (Protein).
Warning: Residue SER23 in chain has different type (Protein) from starting 
residue ALA1 (Protein).
Warning: Residue GLY24 in chain has different type (Protein) from starting 
residue ALA1 (Protein).
Warning: Residue ARG25 in chain has different type (Protein) from starting 
residue ALA1 (Protein).
More than 5 unidentified residues at end of chain - disabling further warnings.
Identified residue CYS20 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS3CYS5   CYS10   CYS20   CYS30
SG18SG36SG75   SG144   SG228
CYS5SG36   0.834
   CYS10SG75   0.936   1.000
   CYS20   SG144   0.833   0.203   0.935
   CYS30   SG228   0.856   0.827   0.200   0.788
   CYS31   SG234   0.202   0.860   0.783   0.820   0.734
Linking CYS-3 SG-18 and CYS-31 SG-234...
Linking CYS-5 SG-36 and CYS-20 SG-144...
Linking CYS-10 SG-75 and CYS-30 SG-228...
Start terminus ALA-1: NH3+
End terminus CYS-20: COO-

Fatal error:
Residue 'EME' not found in residue topology database.


http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database

Jan

Kindly tell me how to over come this error.

Suryanarayana Seera,
PhD student,
Hyderabad,
India.

-- 
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/Search before 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

Re: [gmx-users] Re: One molculetype for 3 proteins

[Steven Neumann]

On Thu, May 24, 2012 at 10:04 PM, Francesca wrote:

> I checked and the resul is the same...but now I know I can use -chainsep
> interactive!
>
>
Yes, it works (-chainsep interactive: merge = no ) but when you process to
grompp there is an error:

Unknown cmap torsion between atoms 6002 6004 6006 6017 6021

pdb2gmx takes the cmap for the atoms e.g. last two residues of chain A with
first three residues of chain B. Does removing this lines will be
reasonable or some torsions wont be taken into account?

Steven


>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/One-molculetype-for-3-proteins-tp4997727p4997739.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> 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/Search before 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
>
-- 
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/Search before 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

[gmx-users] Extraction of low-energy conformations

[Андрей Гончар]

Hello.
How to extract all low-energy conformations from MD-trajectory of protein?

-- 

Андрей Гончар
-- 
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/Search before 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

[gmx-users] Regarding error

[Seera Suryanarayana]

Dear all gromacs users,

  While i am using the commond" pdb2gmx -f
4E82.pdb -o 4E82.gro -p 4E82.top".I am getting the following warnings and
errors.



Warning: Residue EME21 in chain has different type (Other) from starting
residue ALA1 (Protein).
Warning: Residue ILE22 in chain has different type (Protein) from starting
residue ALA1 (Protein).
Warning: Residue SER23 in chain has different type (Protein) from starting
residue ALA1 (Protein).
Warning: Residue GLY24 in chain has different type (Protein) from starting
residue ALA1 (Protein).
Warning: Residue ARG25 in chain has different type (Protein) from starting
residue ALA1 (Protein).
More than 5 unidentified residues at end of chain - disabling further
warnings.
Identified residue CYS20 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS3CYS5   CYS10   CYS20   CYS30
SG18SG36SG75   SG144   SG228
CYS5SG36   0.834
   CYS10SG75   0.936   1.000
   CYS20   SG144   0.833   0.203   0.935
   CYS30   SG228   0.856   0.827   0.200   0.788
   CYS31   SG234   0.202   0.860   0.783   0.820   0.734
Linking CYS-3 SG-18 and CYS-31 SG-234...
Linking CYS-5 SG-36 and CYS-20 SG-144...
Linking CYS-10 SG-75 and CYS-30 SG-228...
Start terminus ALA-1: NH3+
End terminus CYS-20: COO-

Fatal error:
Residue 'EME' not found in residue topology database.

Kindly tell me how to over come this error.

Suryanarayana Seera,
PhD student,
Hyderabad,
India.
-- 
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/Search before 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

[gmx-users] Re: gmx-users Digest, Vol 97, Issue 185

[rethina malliga]

On Thu, May 24, 2012 at 12:49 PM,  wrote:

> Send gmx-users mailing list submissions to
>gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>gmx-users-requ...@gromacs.org
>
> You can reach the person managing the list at
>gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>   1. Tabulated potential 1-4 interactions (mohan maruthi sena)
>   2. Re: ptn ptn interaction (Justin A. Lemkul)
>   3. Re: Justin umbrella sampling tutorial.. (rama david)
>   4. Re: Regarding error. (vivek sharma)
>   5. Re: g_rms -bm (Kowsar Bagherzadeh)
>
>
> --
>
> Message: 1
> Date: Thu, 24 May 2012 11:46:34 +0600
> From: mohan maruthi sena 
> Subject: [gmx-users] Tabulated potential 1-4 interactions
> To: gmx-users@gromacs.org
> Message-ID:
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi all,
>   I am using tabulated potential option  for non bonded
> interactions. The system that i am using contains on CA(alpha) CB(beta)
> ,atoms connected, If i use option
> energygrps = CA CB
> energytable = CA CA CB CB  it caluclates potential
> between CA CA and CB CB , CA CB. I also want to use tabulated potential for
> 1,4 atoms  but this option does not take care of that, so how can i mention
> that option in mdp file so that it uses tabulated potential for 1,4
> interaction also.
>
> Thanks in advance,
>
>
> Regards,
> Mohan
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20120524/c64863c9/attachment-0001.html
>
> --
>
> Message: 2
> Date: Thu, 24 May 2012 07:49:11 +0200
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] ptn ptn interaction
> To: Discussion list for GROMACS users 
> Message-ID: <4fbdcbd7.2090...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 5/24/12 7:43 AM, rethina malliga wrote:
> > Hi,
> >
> > I tried protein protein simulation in gromacs.
> >
> > I prepared one ptn and kept seperately with its .top, .itp, .gro files.
> >
> > Then I prepared another protein and I build the complex of pasting the
> .gro file
> > of first processed protein in the .gro file of second processed ptn.
> >
> > In the topol.top  of second protein I included the molecule type at the
> bottom
> > and inserted
> >;Include ligand topology
> >#include "posre.itp"
> >
>
> Be careful about name clashes here - the first protein (by default) will
> have a
> file named "posre.itp" that will be applied to it.  If you use the same
> name for
> different files, you'll probably get other errors.  I find it useful to
> call
> everything based on specific names, like "posre_proteinA.itp" or something
> similar.
>
> > And i run succeccfully the newbox generation, solvent adding commands.
> >
> > But with the ions adding command it shows fatal error that the atoms in
> > topol.top and solv.gro is different.
> >
> > `Fatal error:
> > number of coordinates in coordinate file (solv.gro, 231262)
> >   does not match topology (topol.top, 237548)
> >
> > on analysing the difference between two files i come to know that it is
> taking
> > the atoms of first protein for the second protein though i named first
> and
> > second proteins different.
> >
>
> After you added the second protein, did you correctly update the
> [molecules]
> section of the topology?
>
> > I changed the residue information in .gro of first file to 1LIG and
> change
> > everything regarding second molecules name as 1LIG
> >
>
> Unless your protein residues are all called LIG, then this is not
> appropriate.
>
> > and after retrying the ions adding command it says no such molecule type
> found.
> >
> > `Fatal error:
> > No such moleculetype 1LIG
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
>
> This comes from incorrect naming.  Updating [molecules] correctly with the
> name
> of your second protein [moleculetype] will solve it.  Make sure you make
> changes
> to both the coordinate file and topology at all steps - they should always
> match.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
> --
>
> Message: 3
> Date: Thu, 24 May 2012 11:49:07 +0530
> From: rama david 
> Subject: Re: [gmx-users] Ju

[gmx-users] unknown cmap torsion between atoms

[Steven Neumann]

Dear Gmx Users,

My system is made of 3 proteins. As I want to use distance restraints
dynamics between atoms belonging to each of them I have to produce topoloy
with one moleculetype. I used pdb2gmx -chainsep interactive (I used merge:
yes).

Then when I process to grompp the error: "unknown cmap torsion between
atoms  ..."

These atoms belong to the last residue of the chain A and to the first
residue of Chain B. How to get rid of this? Please, help.

Steven
-- 
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/Search before 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

[gmx-users] electrostatic component of the forces

[Julian Mondon-Garrec]

Hi all,

I am trying to get the electrostatic forces acting on each atom as a 
function of time. I have checked the list and all the suggestions are 
based on rerunning the simulation. Is there not an easy way to print 
these forces on the fly ? If not, what is the cleanest way to remove 
bonded and vdw components from the forces ? One option could be to set 
all the unwanted interaction to zero in the topology file but I am 
wondering if there is a safer alternative.


Cheers,

--
Julian Garrec, post-doc

Tel: ++41 (0)21 69 303 27
Web: https://sites.google.com/site/juliangarrec/

Laboratory of Computational Chemistry and Biochemistry
BCH 4201 Ecole Polytechnique Fédérale de Lausanne
CH-1015 Lausanne

--
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/Search before 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

Re: [gmx-users] Re: One molculetype for 3 proteins

[Steven Neumann]

Yes, it works (-chainsep interactive: merge = yes ) but when you process to
grompp there is an error:

Unknown cmap torsion between atoms 6002 6004 6006 6017 6021

pdb2gmx takes the cmap for the atoms e.g. last two residues of chain A with
first three residues of chain B. Removing these lines does not solve the
problem. Any suggestions appreciated!



On Fri, May 25, 2012 at 9:57 AM, Steven Neumann wrote:

>
>
> On Thu, May 24, 2012 at 10:04 PM, Francesca 
> wrote:
>
>> I checked and the resul is the same...but now I know I can use -chainsep
>> interactive!
>>
>>
> Yes, it works (-chainsep interactive: merge = no ) but when you process to
> grompp there is an error:
>
> Unknown cmap torsion between atoms 6002 6004 6006 6017 6021
>
> pdb2gmx takes the cmap for the atoms e.g. last two residues of chain A
> with first three residues of chain B. Does removing this lines will be
> reasonable or some torsions wont be taken into account?
>
> Steven
>
>
>>
>> --
>> View this message in context:
>> http://gromacs.5086.n6.nabble.com/One-molculetype-for-3-proteins-tp4997727p4997739.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>> --
>> 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/Search before 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
>>
>
>
-- 
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/Search before 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