date:20130321

That's probably a free-energy plot, made by some tool that works like
g_sham. Every structure can be projected onto the coordinates of the
underlying 2D histogram.

Mark

On Thu, Mar 21, 2013 at 10:42 AM, Albert mailmd2...@gmail.com wrote:

 Hello:

  I've finished a replica exchange simulation and I would  like to make a
 plot like:


 http://ars.els-cdn.com/**content/image/1-s2.0-**S1093326303002006-gr4.jpghttp://ars.els-cdn.com/content/image/1-s2.0-S1093326303002006-gr4.jpg

 I am just wondering how can associate your energy (the red/white color)
 with 2D XY plot in the above figure?

 thank you very much
 best
 Albert

 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
 * Please search the archive at http://www.gromacs.org/**
 Support/Mailing_Lists/Searchhttp://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_Listshttp://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] Top file modification

Dears,

As I read in some other messages in mailing list, it is supposed to modify 
bonds, angles and dihedrals in top file to define a peptide bond for the last 
and first residues as well as other peptide bonds.
I am wondering if it is necessary to define pairs too? 

Thanks in advance.



Sincerely,
Shima



From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com 
Cc: Discussion list for GROMACS users gmx-users@gromacs.org 
Sent: Tuesday, March 19, 2013 9:11 PM
Subject: Re: [gmx-users] Top file modification





On Tue, Mar 19, 2013 at 1:36 PM, Shima Arasteh shima_arasteh2...@yahoo.com 
wrote:

Would you please let me know if it is acceptable to add dihedrals and angles 
and bonds? and not to add any pairs to the top? just deleting the pairs which 
are added by pdb2gmx incorrectly to the terminus?


And I don't know that if I don't add all bonds or dihedrals what would happen? 
How would I be sure that I have added all modifications completely?



All you're doing is creating a peptide bond like any other. Its description 
should be identical to any other peptide bond in the protein. An incorrect or 
incomplete description of the newly created peptide bond would mean an 
unreliable physical model that would either crash or produce spurious results.

-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] help with chromophore of a GFP

On Wed, Mar 20, 2013 at 6:01 PM, Anna MARABOTTI amarabo...@unisa.it wrote:



 Dear gmx-users,

 it's about two weeks that I'm trying to solve this
 problem, and I can't, so I'm asking your help.

 I want to do some MD
 simulations on a protein of the family of green fluorescent protein.
 This protein, as you know, has a chromophore (CFY) derived from four
 residues of the protein (F64-C65-Y66-G67) and covalently bound to the
 rest of the protein chain. How to parametrize this object, since it is
 not recognized by pdb2gmx? I looked at the gmx-users list and the
 suggestion was to create a new entry in the .rtp file of the selected
 forcefield.


Indeed, this kind of problem is most easily solved by making a new
residue that contains the whole chromophore, such that it links to its
neighbours with normal peptide links.


 I decided to use Amber99SB since it seemed the better for my
 scope, then I start trying to parameterize it. This is what I did:

 *


 I used Pymol to add H to my pdb file, since I want to use an all H
 forcefield and since Antechamber (see below) does not work without H
 *


 I extracted the segment V63-CFY-H68 from my .pdb file. I did this
 since, when I extracted CFY only, I had problems with the terminals
 *


 Following the Antechamber tutorial, I used Antechamber (using the
 traditional Amber force field, not GAFF) to calculate charges and to
 assign atom types to this segment.
 *

 I used these calculated
 parameters in order to add the CFY residue to aminoacids.rtp in
 amber99sb.ff directory.
 *

 I tried to modify also aminoacids.hdb, but
 since it seemed too complicated to me, I decided to keep it unchanged,
 and to give pdb2gmx the protein with H already present
 *

 No need to
 add new atom/bond types to ffbonded.itp and ffnonbonded.itp: they seem
 all present. Since CFY is bound to the rest of protein with common
 peptide bonds, I did not change specbond.dat either.
 *

 I added CFY
 in residuetypes.dat with the specification Protein

 In my opinion,
 all was ready to go, instead...

 When I launched pdb2gmx to my protein
 with H added by PyMol, I got immediately an error:

 Fatal error:

 Atom
 H01 in residue SER 3 was not found in rtp entry NSER with 13 atoms


 while sorting atoms.

 For a hydrogen, this can be a different
 protonation state, or it

 might have had a different number in the PDB
 file and was rebuilt

 (it might for instance have been H3, and we only
 expected H1  H2).

 Note that hydrogens might have been added to the
 entry for the N-terminus.

 Remove this hydrogen or choose a different
 protonation state to solve it.

 Option -ignh will ignore all hydrogens
 in the input.

 For more information and tips for troubleshooting,
 please check the GROMACS

 website at
 http://www.gromacs.org/Documentation/Errors [1]

 From this error I
 understand that:

 *

 the code for H in PyMol is different from the
 code for H in Amber (read from aminoacids.rtp); in order to correct this
 error, I should add -ignh in order to ignore H in input.


pdb2gmx has to be able to make sense of the atom naming. There are lots of
different conventions for how to name atoms, particularly hydrogen atoms.
pdb2gmx can't possibly encode the logic to convert all of those
conventions. So the path of least resistance can be to ignore hydrogens and
regenerate them according to the generation rules.

However, you can just rename them in the input file so that pdb2gmx
understands your meaning. The NSER entry in the .rtp file shows you the
names pdb2gmx expects. If you edit the names of those hydrogen atoms
(probably H01, H02, H03) in your input coordinate file accordingly (to H1,
H2, H3), things will be fine. Be sure you don't break the required column
formatting of the coordinate file!

*

 If I add
 -ignh, all the H of CFY will be ignored too, and I will not be able to
 add them since I did not modify aminoacids.hdb
 *

 since I made
 calculations on CFY with H added by PyMol, probably also my codes for H
 will be wrong.


Your atom names for CFY in the .rtp and the input coordinate file will have
to match. How you want to achieve that is up to you.


 *

 If I use reduce (the Amber tool to add H, as
 suggested by the tutorial) to add H to my protein, it does not add H to
 CFY because it complaints that the residue is not in HETATM connection
 database (but the record CONECT is present in .pdb file). If I add H to
 CFY alone, I have problems with the terminals.

 My question is,
 obviously: how can I parameterize this chromophore correctly? Please
 give me, if possible, some step-by-step indications on what to do. I
 made dozens of trials, ALL with errors, and I really do not know how to
 do.


You're very much on the right track.

Your decision to use Pymol to generate main chain hydrogens rather than
teach pdb2gmx how to generate CFY hydrogens had consequences that you are
now dealing with. In a

Re: [gmx-users] Restraining water molecule

On 3/21/13 4:29 AM, neeru sharma wrote:

Message: 6
Date: Wed, 20 Mar 2013 09:04:05 -0400
From: Justin Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Restraining water molecule
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:

caduqwc5+fotchpmi0pqeexcnpkbtqa-yb0px1p889gy3jza...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1

On Wed, Mar 20, 2013 at 8:57 AM, neeru sharma neeru.bioi...@gmail.com

wrote:

Dear gromacs users,

I am simulating a system of Protein-ion-GTP with One Water molecule. I

want

to restrain this system (along with this water molecule) for minimization
and equilibration.

Everytime I run this by specifying the .itp files, it gives the error of
misplacement as follows:

*This probably means that you have inserted topology section
position_restraints
in a part belonging to a different molecule than you intended to.
In that case move the position_restraints section to the right

molecule.

*

The sequence I am giving in the topology file is like this:

*
; Include Position restraint file for Protein-ion-GTP-Water
#ifdef POSRES_LIGAND
#include posre_comp.itp
#endif

; Include ligand topology
#include gtp.itp

; Include water topology
#include gromos43a1.ff/spc.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
#endif

; Include topology for ions
#include gromos43a1.ff/ions.itp*
*

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein 1
GTP 1
SOL 1
SOL   12179
NA   8
*

Can anybody help me figuring out the issue,where I am doing wrong? Any
suggestion is welcome

If you want to restrain a single water molecule, it needs to be defined as
its own [moleculetype] or as a part of the protein [moleculetype]. Breaking
apart a continuous block of water causes problems with the SETTLE
algorithm, so you will need to manually specify three constraints (OW-HW1,
OW-HW2, and HW1-HW2) for this water molecule, while the remaining bath of
solvent would be handled by SETTLE.

-Justin

--

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

--

--
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!

End of gmx-users Digest, Vol 107, Issue 81
**

I tried restraining the single water molecule by specifying the
Protein-Ion-GTP-Water as one index group. The itp file, I used for this
water molecule was as follows:

*[ moleculetype ]
; molname   nrexcl
WAT 2

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
#ifndef HEAVY_H
  1  O  1WAT  O  1  -0.82   15.99940
  2  H  1WAT H1  1   0.411.00800
  3  H  1WAT H2  1   0.411.00800
#else
  1  O  1WAT  O  1  -0.829.95140
  2  H  1WAT H1  1   0.414.03200
  3  H  1WAT H2  1   0.414.03200
#endif

#ifndef FLEXIBLE
[ settles ]
; O funct   doh dhh
1   1   0.1 0.16330

[ exclusions ]
1   2   3
2   1   3
3   1   2
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.1 345000  0.1 345000
1   3   1   0.1 345000  0.1 345000

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   109.47  383 109.47  383
#endif*

But, ended with the fatal error:

*Fatal error:
The [molecules] section of your topology specifies more than one block of
a [moleculetype] with a [settles] block. Only one such is allowed. If you
are trying to partition your solvent into different *groups* (e.g. for
freezing, T-coupling, etc.) then you are using the wrong approach. Index
files specify groups. Otherwise, you may wish to change the least-used
block of molecules with SETTLE constraints into 3 normal constraints.*

Then, I tried removed the settles block:

*[ settles ]
; O funct   doh dhh
1   1   0.1 0.16330

*from the itp file. It then, ran the minimization steps which continued for
40 steps. But when I visualized the gro file generated, the conformation
and orientation of this particular water molecule was not proper. I feel, I
the settle section of itp file was not treated properly.

Any suggestion how to treat this water molecule?

Yes, read my post again.  I already said this would happen and described exactly

Re: [gmx-users] Re: freeze the particular residues in NPT-NVT




On 3/21/13 2:12 AM, 라지브간디 wrote:


p{margin:0;padding:0;}




Dear Justin,


I have checked my index.ndx file and it doesnt have any atoms close to 37872 
atoms. I am bit confused why its happening.



There is some colossal mismatch between your coordinates, topology, and/or index 
file.  I would recommend eliminating all the freezing and special groups and try 
to get a vanilla system working, then add complexity with the groups you're 
trying to freeze.  There's something more fundamentally wrong here that you need 
to be solving first.


-Justin





Contents of index file fz.ndx
--
Nr.   Group   #Entries   FirstLast
0  System  2124   12124
1  Protein 1522   11522
2  Protein-H   1204   11522
3  C-alpha  151   51506
4  Backbone 453   11520
5  MainChain605   11522
6  MainChain+Cb 746   11522
7  MainChain+H  754   11522
8  SideChain768   61519
9  SideChain-H  599   61518
   10  Prot-Masses 1522   11522
   11  non-Protein  60215232124
   12  Other 5915231581
   13  SO4   1015231532
   14  HEM   4715331579
   15  CMO215801581
   16  Water54315822124
   17  SOL  54315822124
   18  non-Water   1581   11581
   19  g110  28  37
   20  g212  74  85
   21  g312 241 252
   22  g417 289 305
   23  g510 400 409
   24  g617 423 439
   25  g717 449 465
   26  g817 466 482
   27  g913 483 495
   28  g109 508 516
   29  g11   13 574 586
   30  g129 620 628
   31  g13   13 642 654
   32  g14   12 655 666
   33  g15   12 897 908
   34  g16   13 944 956
   35  g17   1010911100
   36  g18911451153
   37  g19   1211541165
   38  g20811661173
   39  g21   1711741190
   40  g22912541262
   41  g23   1212691280
   42  g24   1313121324
   43  g25   1013401349
   44  g26   1713591375
   45  g27914151423
   46  g28   1814491466
   47  g29   1915041522








Usually the Protein Non-Protein approach covers everything. Apparently in
your case, something is wrong and you will have to figure out what has not
been accounted for. Try using gmxcheck on your index file to see if there
is a group (or groups) whose contents account for 37872 atoms.

-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] Reg: Validation of Protein-Protein Interaction through simulation




On 3/21/13 5:11 AM, Amit wrote:

Dear Gromacs Users,
 I am new to gromacs software  and
currently in learning phase. Currently, I am facing a big problem. I have
two proteins namely A and B. Wet lab results have shown that both A and B
interacts with each other by co-immunoprecipitation techniques. Is there a
way out to know weather protein A really interacts with B through
simulation? Is it possible to simulate both the proteins together in a
single box without doing docking? Can simulation provide the interacting
regions? I want to incorporate both the proteins together in box without
docking. Please correct me if I am wrong.



Depending on the size of the proteins, doing an unbiased simulation of 
protein-protein binding may or may not be feasible.  There is a high probability 
of nonspecific interactions, which may or may not be relevant.  If you bias the 
simulation towards interacting in some preconceived way, then the simulation 
doesn't show much more than the fact that it did what you told it to do.


-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] Top file modification




On 3/21/13 6:30 AM, Shima Arasteh wrote:

Dears,

As I read in some other messages in mailing list, it is supposed to modify 
bonds, angles and dihedrals in top file to define a peptide bond for the last 
and first residues as well as other peptide bonds.
I am wondering if it is necessary to define pairs too?



If pairs are a necessary part of the force field, then yes.  Look at the 
formulation of peptide bonds that you have not messed with to learn what is 
expected.


-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: Reg: Validation of Protein-Protein Interaction through simulation

2013-03-21 Thread Amit

Dear Dr. Lemkul,
Many thanks for the reply and suggestion. I
believe doing docking first and then going for simulation is more
relevant as this will lessen the nonspecific interaction. Correct me
if I am wrong. Also I would like to ask one more question. I would
like to simulate gold nanoparticle and protein together. So how can i
prepare the .pdb and topology file for the nanoparticle as it is
composed of charged atoms? Please let me know.

On Thu, Mar 21, 2013 at 4:42 PM, Justin Lemkul [via GROMACS]
ml-node+s5086n5006519...@n6.nabble.com wrote:

On 3/21/13 5:11 AM, Amit wrote:

Dear Gromacs Users,
I am new to gromacs software and
currently in learning phase. Currently, I am facing a big problem. I have
two proteins namely A and B. Wet lab results have shown that both A and B
interacts with each other by co-immunoprecipitation techniques. Is there a
way out to know weather protein A really interacts with B through
simulation? Is it possible to simulate both the proteins together in a
single box without doing docking? Can simulation provide the interacting
regions? I want to incorporate both the proteins together in box without
docking. Please correct me if I am wrong.

Depending on the size of the proteins, doing an unbiased simulation of
protein-protein binding may or may not be feasible. There is a high
probability
of nonspecific interactions, which may or may not be relevant. If you bias
the
simulation towards interacting in some preconceived way, then the simulation
doesn't show much more than the fact that it did what you told it to do.

-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 list[hidden email]
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 [hidden email].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

If you reply to this email, your message will be added to the discussion
below:
http://gromacs.5086.n6.nabble.com/Reg-Validation-of-Protein-Protein-Interaction-through-simulation-tp5006514p5006519.html
To unsubscribe from Reg: Validation of Protein-Protein Interaction through
simulation, click here.
NAML

Yours Sincerely,

Amit Jaiswal,
Department of Bioinformatics,
School of Life Sciences,
Pondicherry Central University,
Kalapet, Pondicherry,
Puducherry - 605 014.
Phone No.: +91 8124954834.

--
View this message in context:
http://gromacs.5086.n6.nabble.com/Reg-Validation-of-Protein-Protein-Interaction-through-simulation-tp5006514p5006521.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: Reg: Validation of Protein-Protein Interaction through simulation

On 3/21/13 7:38 AM, Amit wrote:

That approach is probably more reasonable.

like to simulate gold nanoparticle and protein together. So how can i
prepare the .pdb and topology file for the nanoparticle as it is
composed of charged atoms? Please let me know.

You need a force field that can handle both protein and gold parameters. None
exist by default in Gromacs, but you can introduce new force fields if needed.
There are many posts about such topics in the list archive, but if you are new
to Gromacs, you should probably invest significant time learning how things work
and how the force fields are organized before you try implementing a custom
force field. Doing so is a rather advanced task and require thorough knowledge
of how everything works.

-Justin

On Thu, Mar 21, 2013 at 4:42 PM, Justin Lemkul [via GROMACS]
ml-node+s5086n5006519...@n6.nabble.com wrote:

On 3/21/13 5:11 AM, Amit wrote:

-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] Restraining water molecule

2013-03-21 Thread neeru sharma

 Message: 1
 Date: Thu, 21 Mar 2013 07:05:44 -0400
 From: Justin Lemkul jalem...@vt.edu
 Subject: Re: [gmx-users] Restraining water molecule
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID: 514ae988.4050...@vt.edu
 Content-Type: text/plain; charset=ISO-8859-1; format=flowed

 On 3/21/13 4:29 AM, neeru sharma wrote:
  Message: 6
  Date: Wed, 20 Mar 2013 09:04:05 -0400
  From: Justin Lemkul jalem...@vt.edu
  Subject: Re: [gmx-users] Restraining water molecule
  To: Discussion list for GROMACS users gmx-users@gromacs.org
  Message-ID:

  caduqwc5+fotchpmi0pqeexcnpkbtqa-yb0px1p889gy3jza...@mail.gmail.com
  Content-Type: text/plain; charset=ISO-8859-1

  On Wed, Mar 20, 2013 at 8:57 AM, neeru sharma neeru.bioi...@gmail.com
  wrote:

  Dear gromacs users,

  I am simulating a system of Protein-ion-GTP with One Water molecule. I
  want
  to restrain this system (along with this water molecule) for
 minimization
  and equilibration.

  Everytime I run this by specifying the .itp files, it gives the error
 of
  misplacement as follows:

  *This probably means that you have inserted topology section
  position_restraints
  in a part belonging to a different molecule than you intended to.
  In that case move the position_restraints section to the right
  molecule.
  *

  The sequence I am giving in the topology file is like this:

  *
  ; Include Position restraint file for Protein-ion-GTP-Water
  #ifdef POSRES_LIGAND
  #include posre_comp.itp
  #endif

  ; Include ligand topology
  #include gtp.itp

  ; Include water topology
  #include gromos43a1.ff/spc.itp

  #ifdef POSRES_WATER
  ; Position restraint for each water oxygen
  [ position_restraints ]
  ;  i funct   fcxfcyfcz
  11   1000   1000   1000
  #endif

  ; Include topology for ions
  #include gromos43a1.ff/ions.itp*
  *

  [ system ]
  ; Name
  Protein in water

  [ molecules ]
  ; Compound#mols
  Protein 1
  GTP 1
  SOL 1
  SOL   12179
  NA   8
  *

  Can anybody help me figuring out the issue,where I am doing wrong? Any
  suggestion is welcome

  If you want to restrain a single water molecule, it needs to be defined
 as
  its own [moleculetype] or as a part of the protein [moleculetype].
 Breaking
  apart a continuous block of water causes problems with the SETTLE
  algorithm, so you will need to manually specify three constraints
 (OW-HW1,
  OW-HW2, and HW1-HW2) for this water molecule, while the remaining bath
 of
  solvent would be handled by SETTLE.

  -Justin

  --

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

  --

  --
  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!

  End of gmx-users Digest, Vol 107, Issue 81
  **

  I tried restraining the single water molecule by specifying the
  Protein-Ion-GTP-Water as one index group. The itp file, I used for this
  water molecule was as follows:

  *[ moleculetype ]
  ; molname   nrexcl
  WAT 2

  [ atoms ]
  ;   nr   type  resnr residue  atom   cgnr charge   mass
  #ifndef HEAVY_H
1  O  1WAT  O  1  -0.82   15.99940
2  H  1WAT H1  1   0.411.00800
3  H  1WAT H2  1   0.411.00800
  #else
1  O  1WAT  O  1  -0.829.95140
2  H  1WAT H1  1   0.414.03200
3  H  1WAT H2  1   0.414.03200
  #endif

  #ifndef FLEXIBLE
  [ settles ]
  ; O funct   doh dhh
  1   1   0.1 0.16330

  [ exclusions ]
  1   2   3
  2   1   3
  3   1   2
  #else
  [ bonds ]
  ; i j   funct   length  force.c.
  1   2   1   0.1 345000  0.1 345000
  1   3   1   0.1 345000  0.1 345000

  [ angles ]
  ; i j   k   funct   angle   force.c.
  2   1   3   1   109.47  383 109.47  383
  #endif*

  But, ended with the fatal error:

  *Fatal error:
  The [molecules] section of your topology specifies more than one block of
  a [moleculetype] with a [settles] block. Only one such is allowed. If you
  are trying to partition your solvent into different *groups* (e.g. for
  freezing, T-coupling, etc.) then you are using the wrong approach. Index
  files specify groups. Otherwise, you may wish to change the least-used
  block of molecules

Re: [gmx-users] Restraining water molecule

On 3/21/13 8:10 AM, neeru sharma wrote:

Message: 1
Date: Thu, 21 Mar 2013 07:05:44 -0400
From: Justin Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Restraining water molecule
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 514ae988.4050...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 3/21/13 4:29 AM, neeru sharma wrote:

Message: 6
Date: Wed, 20 Mar 2013 09:04:05 -0400
From: Justin Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Restraining water molecule
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:

caduqwc5+fotchpmi0pqeexcnpkbtqa-yb0px1p889gy3jza...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1

On Wed, Mar 20, 2013 at 8:57 AM, neeru sharma neeru.bioi...@gmail.com

wrote:

Dear gromacs users,

I am simulating a system of Protein-ion-GTP with One Water molecule. I

want

to restrain this system (along with this water molecule) for

minimization

and equilibration.

Everytime I run this by specifying the .itp files, it gives the error

of

misplacement as follows:

*This probably means that you have inserted topology section
position_restraints
in a part belonging to a different molecule than you intended to.
In that case move the position_restraints section to the right

molecule.

*

The sequence I am giving in the topology file is like this:

*
; Include Position restraint file for Protein-ion-GTP-Water
#ifdef POSRES_LIGAND
#include posre_comp.itp
#endif

; Include ligand topology
#include gtp.itp

; Include water topology
#include gromos43a1.ff/spc.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
 11   1000   1000   1000
#endif

; Include topology for ions
#include gromos43a1.ff/ions.itp*
*

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein 1
GTP 1
SOL 1
SOL   12179
NA   8
*

Can anybody help me figuring out the issue,where I am doing wrong? Any
suggestion is welcome

If you want to restrain a single water molecule, it needs to be defined

as

its own [moleculetype] or as a part of the protein [moleculetype].

Breaking

apart a continuous block of water causes problems with the SETTLE
algorithm, so you will need to manually specify three constraints

(OW-HW1,

OW-HW2, and HW1-HW2) for this water molecule, while the remaining bath

of

solvent would be handled by SETTLE.

-Justin

--

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

--

--
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!

End of gmx-users Digest, Vol 107, Issue 81
**

I tried restraining the single water molecule by specifying the
Protein-Ion-GTP-Water as one index group. The itp file, I used for this
water molecule was as follows:

*[ moleculetype ]
; molname   nrexcl
WAT 2

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
#ifndef HEAVY_H
   1  O  1WAT  O  1  -0.82   15.99940
   2  H  1WAT H1  1   0.411.00800
   3  H  1WAT H2  1   0.411.00800
#else
   1  O  1WAT  O  1  -0.829.95140
   2  H  1WAT H1  1   0.414.03200
   3  H  1WAT H2  1   0.414.03200
#endif

#ifndef FLEXIBLE
[ settles ]
; O funct   doh dhh
1   1   0.1 0.16330

[ exclusions ]
1   2   3
2   1   3
3   1   2
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.1 345000  0.1 345000
1   3   1   0.1 345000  0.1 345000

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   109.47  383 109.47  383
#endif*

But, ended with the fatal error:

*Fatal error:
The [molecules] section of your topology specifies more than one block of
a [moleculetype] with a [settles] block. Only one such is allowed. If you
are trying to partition your solvent into different *groups* (e.g. for
freezing, T-coupling, etc.) then you are using the wrong approach. Index
files specify groups. Otherwise, you may wish to change the least-used
block of molecules with SETTLE constraints into 3 normal constraints.*

Then, I tried removed the settles block:

*[ settles ]
; O funct   doh dhh
1   1   0.1 0.16330

*from the itp file. It then, ran the minimization steps which

[gmx-users] T-Coupling groups in NVT

Hi,

I am simulating a system of POPC/Water/Ions/protein.
Ions are 1 M NaCL and 3 CL atoms to neutralize the system.

In NVT step, I have coupling groups as :
tc-grps        = Protein POPC    SOL_CL    

comm_grps    = Protein_POPC SOL_CL

when I run the grompp for NVT, I get the error that the 615 Na atoms are not 
part of any of the T-Coupling groups.

Now, I 'd like to know if I need to couple Na with SOL_CL such as SOL_CL-Na ? 
Or I need to create a seperate group for Na?

Would you please give me suggestions?
Thanks in advance.

 
Sincerely,
Shima
--
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] T-Coupling groups in NVT

On Thu, Mar 21, 2013 at 8:56 AM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote:

 Hi,

 I am simulating a system of POPC/Water/Ions/protein.
 Ions are 1 M NaCL and 3 CL atoms to neutralize the system.

 In NVT step, I have coupling groups as :
 tc-grps= Protein POPCSOL_CL

 comm_grps= Protein_POPC SOL_CL

 when I run the grompp for NVT, I get the error that the 615 Na atoms are
 not part of any of the T-Coupling groups.

 Now, I 'd like to know if I need to couple Na with SOL_CL such as
 SOL_CL-Na ? Or I need to create a seperate group for Na?


Ions should never be coupled separately from the solvent. You coupled Cl-
with water, why wouldn't you do the same for Na+?

http://www.gromacs.org/Documentation/Terminology/Thermostats

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://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] T-Coupling groups in NVT

2013-03-21 Thread Gunther Lukat

I general, I have good results with coupling Ions together with the water. 


Dipl.-Inf. Gunther Lukat
g.lu...@gmx.net
www.aplvoro.org



Am 21.03.2013 um 13:56 schrieb Shima Arasteh shima_arasteh2...@yahoo.com:

 Hi,
 
 I am simulating a system of POPC/Water/Ions/protein.
 Ions are 1 M NaCL and 3 CL atoms to neutralize the system.
 
 In NVT step, I have coupling groups as :
 tc-grps= Protein POPCSOL_CL
 
 comm_grps= Protein_POPC SOL_CL
 
 when I run the grompp for NVT, I get the error that the 615 Na atoms are not 
 part of any of the T-Coupling groups.
 
 Now, I 'd like to know if I need to couple Na with SOL_CL such as SOL_CL-Na ? 
 Or I need to create a seperate group for Na?
 
 Would you please give me suggestions?
 Thanks in advance.
 
  
 Sincerely,
 Shima
 --
 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] T-Coupling groups in NVT

So accordance with Justin's and your statement, SOL_CL_NA coupling would be a 
proper option. right?


Thanks for your suggestions

Sincerely,
Shima



From: Gunther Lukat g.lu...@gmx.net
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS 
users gmx-users@gromacs.org 
Sent: Thursday, March 21, 2013 4:31 PM
Subject: Re: [gmx-users] T-Coupling groups in NVT


I general, I have good results with coupling Ions together with the water. 




Dipl.-Inf. Gunther Lukat
g.lu...@gmx.net
www.aplvoro.org



Am 21.03.2013 um 13:56 schrieb Shima Arasteh shima_arasteh2...@yahoo.com:

Hi,

I am simulating a system of POPC/Water/Ions/protein.
Ions are 1 M NaCL and 3 CL atoms to neutralize the system.

In NVT step, I have coupling groups as :
tc-grps        = Protein POPC    SOL_CL    

comm_grps    = Protein_POPC SOL_CL

when I run the grompp for NVT, I get the error that the 615 Na atoms are not 
part of any of the T-Coupling groups.

Now, I 'd like to know if I need to couple Na with SOL_CL such as SOL_CL-Na ? 
Or I need to create a seperate group for Na?

Would you please give me suggestions?
Thanks in advance.

 
Sincerely,
Shima
--
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
 
--
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] g_tune_pme can't be executed

2013-03-21 Thread Daniel Wang

Hi everyone~

When I run g_tune_pme_mpi, it prompts:

Fatal error:
Need an MPI-enabled version of mdrun. This one
(mdrun_mpi)
seems to have been compiled without MPI support.

I'm sure my gromacs is compiled WITH MPI support and mpiexec -n xx
mdrun_mpi -s yy.tpr works normally.
How to fix it? I'm using gromacs4.6 and Intel MPI 4.1.0.
Thanks.

-- 
Daniel Wang / npbool
Computer Science  Technology, Tsinghua University
-- 
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] g_tune_pme can't be executed

2013-03-21 Thread Carsten Kutzner

Hi Daniel,

are you using the newest version of 4.6? There was an issue with g_tune_pme,
which I already fixed. I guess it could be responsible for the error that 
you see.

Best,
  Carsten


On Mar 21, 2013, at 2:26 PM, Daniel Wang iwnk...@gmail.com wrote:

 Hi everyone~
 
 When I run g_tune_pme_mpi, it prompts:
 
 Fatal error:
 Need an MPI-enabled version of mdrun. This one
 (mdrun_mpi)
 seems to have been compiled without MPI support.
 
 I'm sure my gromacs is compiled WITH MPI support and mpiexec -n xx
 mdrun_mpi -s yy.tpr works normally.
 How to fix it? I'm using gromacs4.6 and Intel MPI 4.1.0.
 Thanks.
 
 -- 
 Daniel Wang / npbool
 Computer Science  Technology, Tsinghua University
 -- 
 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


--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

--
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] g_tune_pme can't be executed

2013-03-21 Thread Daniel Wang

Hi Carsten,

  Actually I tried 4.6.1 weeks ago. Howerev, it seems slighty slower than
old version. It's lucky that I haven't deleted the 4.6.1 build from my
disk. I'm now testing the newest g_tune_pme. It starts up normally but I
have to wait to see the result.
   Thanks a lot!

2013/3/21 Carsten Kutzner ckut...@gwdg.de

 Hi Daniel,

 are you using the newest version of 4.6? There was an issue with
 g_tune_pme,
 which I already fixed. I guess it could be responsible for the error that
 you see.

 Best,
   Carsten


 On Mar 21, 2013, at 2:26 PM, Daniel Wang iwnk...@gmail.com wrote:

  Hi everyone~
 
  When I run g_tune_pme_mpi, it prompts:
 
  Fatal error:
  Need an MPI-enabled version of mdrun. This one
  (mdrun_mpi)
  seems to have been compiled without MPI support.
 
  I'm sure my gromacs is compiled WITH MPI support and mpiexec -n xx
  mdrun_mpi -s yy.tpr works normally.
  How to fix it? I'm using gromacs4.6 and Intel MPI 4.1.0.
  Thanks.
 
  --
  Daniel Wang / npbool
  Computer Science  Technology, Tsinghua University
  --
  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


 --
 Dr. Carsten Kutzner
 Max Planck Institute for Biophysical Chemistry
 Theoretical and Computational Biophysics
 Am Fassberg 11, 37077 Goettingen, Germany
 Tel. +49-551-2012313, Fax: +49-551-2012302
 http://www.mpibpc.mpg.de/grubmueller/kutzner
 http://www.mpibpc.mpg.de/grubmueller/sppexa

 --
 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




-- 
王凝枰 Daniel Wang / npbool
Computer Science  Technology, Tsinghua University
--
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] help with chromophore of a GFP

2013-03-21 Thread Anna MARABOTTI

 

Dear Mark, 

thank you for your message. I'm happy to be on the
right track; unfortunately the end point seems to be very far away...


I tried to obtain that CFY hydrogens and protein hydrogens are all
matching the aminoacids.rtp entry, in order to avoid dealing with
aminoacids.hdb. This is what I did: 

- starting from the pdb file of
the protein, I removed CFY entry (prot_noCFY.pdb) 

- I used pdb2gmx to
add H to the protein only: pdb2gmx -f prot_noCFY.pdb -o prot_noCFY_H.pdb
-p topol.top 

- I inserted CFY_H.pdb (obtained with Pymol in a previous
passage in which I added H with Pymol to the protein, including CFY)
into prot_noCFY_H.pdb, obtaining prot_CFY_H.pdb. 

In this way, H atoms
bound to regular residues have been added using Amber99SB, therefore
they are compatible with this ff, and atoms of CFY (previously added
with Pymol) have the same naming convention in aminoacids.rtp (that I
edited using atom types, charges etc. calculated with Antechamber on
this molecule coming from Pymol). Obviously, the atom numbering is not
sequential: the last atom of V63 (the last regular residue before CFY)
is numbered 938, the first atom of H68 (the first regular residue
after CFY) is numbered 939, and the atoms of CFY66 are numbered from 1
to 70. Moreover, since the sequence of atoms in aminoacids.rtp is not
the same as in the coordinates of CFY (I adapted the sequence of atoms
following the format of other residues in aminoacids.rtp), the numbering
of CFY in the prot_CFY_H.pdb is not ordered (1-2-3--69-70) but
disordered (19-54-20-55...49-50-24-25). 

- At this stage, I used
pdb2gmx again to create the topol.top file with all coordinates correct:


pdb2gmx -f prot_CFY_H.pdb -o prot_complete.gro -p topol.top


(selecting amber99sb forcefield and tip3p for water, as recommended
option) 

This is the message error from pdb2gmx: 

Read 'FLUORESCENT
PROTEIN', 3346 atoms
Analyzing pdb file
Splitting PDB chains based on
TER records or changing chain id.
There are 1 chains and 0 blocks of
water and 218 residues with 3346 atoms

 chain #res #atoms
 1 'A' 213
3346 

All occupancies are one
Opening force field file
./amber99sb.ff/atomtypes.atp
Atomtype 1
Reading residue database...
(amber99sb)
Opening force field file
./amber99sb.ff/aminoacids.rtp
Residue 94
Sorting it all out...
Opening
force field file ./amber99sb.ff/dna.rtp
Residue 110
Sorting it all
out...
Opening force field file ./amber99sb.ff/rna.rtp
Residue
126
Sorting it all out...
Opening force field file
./amber99sb.ff/aminoacids.hdb
Opening force field file
./amber99sb.ff/dna.hdb
Opening force field file
./amber99sb.ff/rna.hdb
Opening force field file
./amber99sb.ff/aminoacids.n.tdb
Opening force field file
./amber99sb.ff/aminoacids.c.tdb

Processing chain 1 'A' (3346 atoms, 213
residues)
There are 327 donors and 319 acceptors
There are 539 hydrogen
bonds
Will use HISE for residue 22
Will use HISD for residue 38
Will use
HISE for residue 62
Will use HISE for residue 68
Will use HISD for
residue 109
Will use HISE for residue 119
Will use HISE for residue
172
Will use HISH for residue 193
Will use HISH for residue 197
Will use
HISE for residue 217
Identified residue SER3 as a starting
terminus.
Identified residue SER218 as a ending terminus.
8 out of 8
lines of specbond.dat converted successfully
Special Atom Distance
matrix:
 MET9 MET11 MET15 HIS22 HIS38 MET41 MET47
 SD110 SD149 SD232
NE2317 NE2549 SD596 SD700
 MET11 SD149 0.807
 MET15 SD232 2.279 1.627

HIS22 NE2317 3.707 2.983 1.466
 HIS38 NE2549 1.401 0.928 2.127 3.254

MET41 SD596 1.458 0.665 1.144 2.384 1.001
 MET47 SD700 3.059 2.324 0.995
0.801 2.656 1.761
 MET53 SD777 2.786 1.999 0.990 1.171 2.160 1.373
0.603
 HIS62 NE2917 2.340 1.733 0.833 1.797 1.988 1.236 1.583
 HIS68
NE21002 0.884 0.597 1.466 2.916 1.356 0.885 2.347
 HIS109 NE21638 2.061
1.886 1.380 2.614 2.661 1.862 2.279
 HIS119 NE21803 1.459 0.967 0.923
2.372 1.617 0.812 1.870
 MET135 SD2041 3.480 2.751 1.316 0.606 2.919
2.121 0.993
 MET162 SD2439 2.521 1.976 1.656 2.412 1.855 1.543 2.264

HIS172 NE22588 3.632 2.949 1.894 1.657 2.872 2.338 1.945
 CYS174 SG2623
2.968 2.372 1.452 1.861 2.428 1.848 1.924
 MET189 SD2891 2.167 2.379
2.736 4.000 2.754 2.569 3.722
 HIS193 NE22942 2.003 2.001 2.490 3.686
2.049 2.075 3.396
 HIS197 NE23011 2.012 1.634 1.830 2.896 1.554 1.426
2.614
 HIS217 NE23329 2.545 2.376 2.831 3.805 2.039 2.305 3.575
 MET53
HIS62 HIS68 HIS109 HIS119 MET135 MET162
 SD777 NE2917 NE21002 NE21638
NE21803 SD2041 SD2439
 HIS62 NE2917 1.363
 HIS68 NE21002 2.107 1.482

HIS109 NE21638 2.365 1.568 1.372
 HIS119 NE21803 1.688 0.976 0.584
1.078
 MET135 SD2041 1.057 1.365 2.661 2.490 2.119
 MET162 SD2439 1.878
0.871 1.805 2.246 1.520 1.861
 HIS172 NE22588 1.721 1.401 2.829 2.860
2.359 1.067 1.342
 CYS174 SG2623 1.694 0.725 2.140 2.152 1.681 1.297
0.745
 MET189 SD2891 3.547 2.310 1.858 1.893 1.980 3.627 2.290
 HIS193
NE22942 3.076 1.890 1.639 2.197 1.760 3.221 1.547
 HIS197 NE23011 2.229
1.149 1.407 2.078 1.323 2.401 0.676
 HIS217 NE23329

Re: [gmx-users] help with chromophore of a GFP

On Thu, Mar 21, 2013 at 11:30 AM, Anna MARABOTTI amarabo...@unisa.itwrote:



 Dear Mark,

 thank you for your message. I'm happy to be on the
 right track; unfortunately the end point seems to be very far away...


 I tried to obtain that CFY hydrogens and protein hydrogens are all
 matching the aminoacids.rtp entry, in order to avoid dealing with
 aminoacids.hdb. This is what I did:

 - starting from the pdb file of
 the protein, I removed CFY entry (prot_noCFY.pdb)

 - I used pdb2gmx to
 add H to the protein only: pdb2gmx -f prot_noCFY.pdb -o prot_noCFY_H.pdb
 -p topol.top

 - I inserted CFY_H.pdb (obtained with Pymol in a previous
 passage in which I added H with Pymol to the protein, including CFY)
 into prot_noCFY_H.pdb, obtaining prot_CFY_H.pdb.

 In this way, H atoms
 bound to regular residues have been added using Amber99SB, therefore
 they are compatible with this ff, and atoms of CFY (previously added
 with Pymol) have the same naming convention in aminoacids.rtp (that I
 edited using atom types, charges etc. calculated with Antechamber on
 this molecule coming from Pymol). Obviously, the atom numbering is not
 sequential: the last atom of V63 (the last regular residue before CFY)
 is numbered 938, the first atom of H68 (the first regular residue
 after CFY) is numbered 939, and the atoms of CFY66 are numbered from 1
 to 70. Moreover, since the sequence of atoms in aminoacids.rtp is not
 the same as in the coordinates of CFY (I adapted the sequence of atoms
 following the format of other residues in aminoacids.rtp), the numbering
 of CFY in the prot_CFY_H.pdb is not ordered (1-2-3--69-70) but
 disordered (19-54-20-55...49-50-24-25).

 - At this stage, I used
 pdb2gmx again to create the topol.top file with all coordinates correct:


 pdb2gmx -f prot_CFY_H.pdb -o prot_complete.gro -p topol.top


 (selecting amber99sb forcefield and tip3p for water, as recommended
 option)

 This is the message error from pdb2gmx:

 Read 'FLUORESCENT
 PROTEIN', 3346 atoms
 Analyzing pdb file
 Splitting PDB chains based on
 TER records or changing chain id.
 There are 1 chains and 0 blocks of
 water and 218 residues with 3346 atoms

  chain #res #atoms
  1 'A' 213
 3346

 All occupancies are one
 Opening force field file
 ./amber99sb.ff/atomtypes.atp
 Atomtype 1
 Reading residue database...
 (amber99sb)
 Opening force field file
 ./amber99sb.ff/aminoacids.rtp
 Residue 94
 Sorting it all out...
 Opening
 force field file ./amber99sb.ff/dna.rtp
 Residue 110
 Sorting it all
 out...
 Opening force field file ./amber99sb.ff/rna.rtp
 Residue
 126
 Sorting it all out...
 Opening force field file
 ./amber99sb.ff/aminoacids.hdb
 Opening force field file
 ./amber99sb.ff/dna.hdb
 Opening force field file
 ./amber99sb.ff/rna.hdb
 Opening force field file
 ./amber99sb.ff/aminoacids.n.tdb
 Opening force field file
 ./amber99sb.ff/aminoacids.c.tdb

 Processing chain 1 'A' (3346 atoms, 213
 residues)
 There are 327 donors and 319 acceptors
 There are 539 hydrogen
 bonds
 Will use HISE for residue 22
 Will use HISD for residue 38
 Will use
 HISE for residue 62
 Will use HISE for residue 68
 Will use HISD for
 residue 109
 Will use HISE for residue 119
 Will use HISE for residue
 172
 Will use HISH for residue 193
 Will use HISH for residue 197
 Will use
 HISE for residue 217
 Identified residue SER3 as a starting
 terminus.
 Identified residue SER218 as a ending terminus.
 8 out of 8
 lines of specbond.dat converted successfully
 Special Atom Distance
 matrix:
  MET9 MET11 MET15 HIS22 HIS38 MET41 MET47
  SD110 SD149 SD232
 NE2317 NE2549 SD596 SD700
  MET11 SD149 0.807
  MET15 SD232 2.279 1.627

 HIS22 NE2317 3.707 2.983 1.466
  HIS38 NE2549 1.401 0.928 2.127 3.254

 MET41 SD596 1.458 0.665 1.144 2.384 1.001
  MET47 SD700 3.059 2.324 0.995
 0.801 2.656 1.761
  MET53 SD777 2.786 1.999 0.990 1.171 2.160 1.373
 0.603
  HIS62 NE2917 2.340 1.733 0.833 1.797 1.988 1.236 1.583
  HIS68
 NE21002 0.884 0.597 1.466 2.916 1.356 0.885 2.347
  HIS109 NE21638 2.061
 1.886 1.380 2.614 2.661 1.862 2.279
  HIS119 NE21803 1.459 0.967 0.923
 2.372 1.617 0.812 1.870
  MET135 SD2041 3.480 2.751 1.316 0.606 2.919
 2.121 0.993
  MET162 SD2439 2.521 1.976 1.656 2.412 1.855 1.543 2.264

 HIS172 NE22588 3.632 2.949 1.894 1.657 2.872 2.338 1.945
  CYS174 SG2623
 2.968 2.372 1.452 1.861 2.428 1.848 1.924
  MET189 SD2891 2.167 2.379
 2.736 4.000 2.754 2.569 3.722
  HIS193 NE22942 2.003 2.001 2.490 3.686
 2.049 2.075 3.396
  HIS197 NE23011 2.012 1.634 1.830 2.896 1.554 1.426
 2.614
  HIS217 NE23329 2.545 2.376 2.831 3.805 2.039 2.305 3.575
  MET53
 HIS62 HIS68 HIS109 HIS119 MET135 MET162
  SD777 NE2917 NE21002 NE21638
 NE21803 SD2041 SD2439
  HIS62 NE2917 1.363
  HIS68 NE21002 2.107 1.482

 HIS109 NE21638 2.365 1.568 1.372
  HIS119 NE21803 1.688 0.976 0.584
 1.078
  MET135 SD2041 1.057 1.365 2.661 2.490 2.119
  MET162 SD2439 1.878
 0.871 1.805 2.246 1.520 1.861
  HIS172 NE22588 1.721 1.401 2.829 2.860
 2.359 1.067 1.342
  CYS174 SG2623 1.694 0.725 2.140

[gmx-users] atom numbers in top file

Dear gmx users,

I have modified the top file of my input.pdb. In this modification I have 
deleted 2 atoms, bonds, and diedrals which these deldeted atoms are involved. 
The atom numbers of deleted atoms are 2 and 3.
IN grompp I get a fatal error that the top file has not a consecutive numbers 
and doesn't start from 1.
Would it be possible to solve this problem? Am I supposed to renumber the atoms 
and other things manually? Is there any command to renumber the top file? Or is 
there any other solutions?

your suggestions would be appreciated.

 
Sincerely,
Shima
--
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] GROMACS Constraints

2013-03-21 Thread 256B

Hello Everyone,

I am running MD on a protein with a heme. I want to use gromacs to build a
bond constraint btw a heme and a his. Does anyone know the proper syntax to
do so ?

 - Thank you 



--
View this message in context: 
http://gromacs.5086.n6.nabble.com/GROMACS-Constraints-tp5006536.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] atom numbers in top file




On 3/21/13 2:12 PM, Shima Arasteh wrote:

Dear gmx users,

I have modified the top file of my input.pdb. In this modification I have 
deleted 2 atoms, bonds, and diedrals which these deldeted atoms are involved. 
The atom numbers of deleted atoms are 2 and 3.
IN grompp I get a fatal error that the top file has not a consecutive numbers 
and doesn't start from 1.
Would it be possible to solve this problem? Am I supposed to renumber the atoms 
and other things manually? Is there any command to renumber the top file? Or is 
there any other solutions?



You need to renumber the topology, and all interactions are affected.  Scripting 
is your friend here.  There is no Gromacs program or command that will do this, 
since modifying topologies in such a way is not normal behavior.


-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] GROMACS Constraints




On 3/21/13 3:05 PM, 256B wrote:

Hello Everyone,

I am running MD on a protein with a heme. I want to use gromacs to build a
bond constraint btw a heme and a his. Does anyone know the proper syntax to
do so ?



Consult Chapter 5 of the manual for all topology-related information.

-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] help with chromophore of a GFP

On Thu, Mar 21, 2013 at 4:30 PM, Anna MARABOTTI amarabo...@unisa.it wrote:



 Dear Mark,

 thank you for your message. I'm happy to be on the
 right track; unfortunately the end point seems to be very far away...


 I tried to obtain that CFY hydrogens and protein hydrogens are all
 matching the aminoacids.rtp entry, in order to avoid dealing with
 aminoacids.hdb. This is what I did:

 - starting from the pdb file of
 the protein, I removed CFY entry (prot_noCFY.pdb)

 - I used pdb2gmx to
 add H to the protein only: pdb2gmx -f prot_noCFY.pdb -o prot_noCFY_H.pdb
 -p topol.top

 - I inserted CFY_H.pdb (obtained with Pymol in a previous
 passage in which I added H with Pymol to the protein, including CFY)
 into prot_noCFY_H.pdb, obtaining prot_CFY_H.pdb.

 In this way, H atoms
 bound to regular residues have been added using Amber99SB, therefore
 they are compatible with this ff, and atoms of CFY (previously added
 with Pymol) have the same naming convention in aminoacids.rtp (that I
 edited using atom types, charges etc. calculated with Antechamber on
 this molecule coming from Pymol). Obviously, the atom numbering is not
 sequential: the last atom of V63 (the last regular residue before CFY)
 is numbered 938, the first atom of H68 (the first regular residue
 after CFY) is numbered 939, and the atoms of CFY66 are numbered from 1
 to 70. Moreover, since the sequence of atoms in aminoacids.rtp is not
 the same as in the coordinates of CFY (I adapted the sequence of atoms
 following the format of other residues in aminoacids.rtp), the numbering
 of CFY in the prot_CFY_H.pdb is not ordered (1-2-3--69-70) but
 disordered (19-54-20-55...49-50-24-25).


Seems fine. pdb2gmx is mostly about atom/residue naming. grompp is mostly
about atom/residue/moleculetype ordering.

- At this stage, I used
 pdb2gmx again to create the topol.top file with all coordinates correct:


 pdb2gmx -f prot_CFY_H.pdb -o prot_complete.gro -p topol.top


 (selecting amber99sb forcefield and tip3p for water, as recommended
 option)

 This is the message error from pdb2gmx:

 Read 'FLUORESCENT
 PROTEIN', 3346 atoms
 Analyzing pdb file
 Splitting PDB chains based on
 TER records or changing chain id.
 There are 1 chains and 0 blocks of
 water and 218 residues with 3346 atoms

  chain #res #atoms
  1 'A' 213
 3346


I'd be concerned about the difference in residue count here, but 4.5.4 is
so old I've no idea whose fault this is.


 All occupancies are one
 Opening force field file
 ./amber99sb.ff/atomtypes.atp
 Atomtype 1
 Reading residue database...
 (amber99sb)
 Opening force field file
 ./amber99sb.ff/aminoacids.rtp
 Residue 94
 Sorting it all out...
 Opening
 force field file ./amber99sb.ff/dna.rtp
 Residue 110
 Sorting it all
 out...
 Opening force field file ./amber99sb.ff/rna.rtp
 Residue
 126
 Sorting it all out...
 Opening force field file
 ./amber99sb.ff/aminoacids.hdb
 Opening force field file
 ./amber99sb.ff/dna.hdb
 Opening force field file
 ./amber99sb.ff/rna.hdb
 Opening force field file
 ./amber99sb.ff/aminoacids.n.tdb
 Opening force field file
 ./amber99sb.ff/aminoacids.c.tdb

 Processing chain 1 'A' (3346 atoms, 213
 residues)
 There are 327 donors and 319 acceptors
 There are 539 hydrogen
 bonds
 Will use HISE for residue 22
 Will use HISD for residue 38
 Will use
 HISE for residue 62
 Will use HISE for residue 68
 Will use HISD for
 residue 109
 Will use HISE for residue 119
 Will use HISE for residue
 172
 Will use HISH for residue 193
 Will use HISH for residue 197
 Will use
 HISE for residue 217
 Identified residue SER3 as a starting
 terminus.
 Identified residue SER218 as a ending terminus.
 8 out of 8
 lines of specbond.dat converted successfully
 Special Atom Distance
 matrix:
  MET9 MET11 MET15 HIS22 HIS38 MET41 MET47
  SD110 SD149 SD232
 NE2317 NE2549 SD596 SD700
  MET11 SD149 0.807
  MET15 SD232 2.279 1.627

 HIS22 NE2317 3.707 2.983 1.466
  HIS38 NE2549 1.401 0.928 2.127 3.254

 MET41 SD596 1.458 0.665 1.144 2.384 1.001
  MET47 SD700 3.059 2.324 0.995
 0.801 2.656 1.761
  MET53 SD777 2.786 1.999 0.990 1.171 2.160 1.373
 0.603
  HIS62 NE2917 2.340 1.733 0.833 1.797 1.988 1.236 1.583
  HIS68
 NE21002 0.884 0.597 1.466 2.916 1.356 0.885 2.347
  HIS109 NE21638 2.061
 1.886 1.380 2.614 2.661 1.862 2.279
  HIS119 NE21803 1.459 0.967 0.923
 2.372 1.617 0.812 1.870
  MET135 SD2041 3.480 2.751 1.316 0.606 2.919
 2.121 0.993
  MET162 SD2439 2.521 1.976 1.656 2.412 1.855 1.543 2.264

 HIS172 NE22588 3.632 2.949 1.894 1.657 2.872 2.338 1.945
  CYS174 SG2623
 2.968 2.372 1.452 1.861 2.428 1.848 1.924
  MET189 SD2891 2.167 2.379
 2.736 4.000 2.754 2.569 3.722
  HIS193 NE22942 2.003 2.001 2.490 3.686
 2.049 2.075 3.396
  HIS197 NE23011 2.012 1.634 1.830 2.896 1.554 1.426
 2.614
  HIS217 NE23329 2.545 2.376 2.831 3.805 2.039 2.305 3.575
  MET53
 HIS62 HIS68 HIS109 HIS119 MET135 MET162
  SD777 NE2917 NE21002 NE21638
 NE21803 SD2041 SD2439
  HIS62 NE2917 1.363
  HIS68 NE21002 2.107 1.482

 HIS109 NE21638 2.365 1.568 1.372

Re: [gmx-users] Installing GROMACS4.6.1 on Intel MIC

Yes, you can use any kind of FFTW installation for correct results.
Hardware for which FFTW provides no SIMD acceleration will have to fall
back on the generic FFTW routines. (Or you might consider using MKL (or
MKL's FFTW-wrapper feature), which I'd guess Intel supports on MIC. We are
making MKL easier to use in 4.6.2.)

Mark

On Wed, Mar 20, 2013 at 7:41 AM, Anirban reach.anirban.gh...@gmail.comwrote:

 Dear ALL,

 I am trying to install GROMACS4.6.1 on Intel MIC processors. A question,
 can GROMACS4.6.1 be compiled using FFTW optimization other than SSE/SSE2
 (as Intel MIC does not support SSE2 instructions)?

 Regards,

 Anirban
 --
 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] help with chromophore of a GFP




On 3/21/13 4:43 PM, Mark Abraham wrote:

On Thu, Mar 21, 2013 at 4:30 PM, Anna MARABOTTI amarabo...@unisa.it wrote:




Dear Mark,

thank you for your message. I'm happy to be on the
right track; unfortunately the end point seems to be very far away...


I tried to obtain that CFY hydrogens and protein hydrogens are all
matching the aminoacids.rtp entry, in order to avoid dealing with
aminoacids.hdb. This is what I did:

- starting from the pdb file of
the protein, I removed CFY entry (prot_noCFY.pdb)

- I used pdb2gmx to
add H to the protein only: pdb2gmx -f prot_noCFY.pdb -o prot_noCFY_H.pdb
-p topol.top

- I inserted CFY_H.pdb (obtained with Pymol in a previous
passage in which I added H with Pymol to the protein, including CFY)
into prot_noCFY_H.pdb, obtaining prot_CFY_H.pdb.

In this way, H atoms
bound to regular residues have been added using Amber99SB, therefore
they are compatible with this ff, and atoms of CFY (previously added
with Pymol) have the same naming convention in aminoacids.rtp (that I
edited using atom types, charges etc. calculated with Antechamber on
this molecule coming from Pymol). Obviously, the atom numbering is not
sequential: the last atom of V63 (the last regular residue before CFY)
is numbered 938, the first atom of H68 (the first regular residue
after CFY) is numbered 939, and the atoms of CFY66 are numbered from 1
to 70. Moreover, since the sequence of atoms in aminoacids.rtp is not
the same as in the coordinates of CFY (I adapted the sequence of atoms
following the format of other residues in aminoacids.rtp), the numbering
of CFY in the prot_CFY_H.pdb is not ordered (1-2-3--69-70) but
disordered (19-54-20-55...49-50-24-25).



Seems fine. pdb2gmx is mostly about atom/residue naming. grompp is mostly
about atom/residue/moleculetype ordering.

- At this stage, I used

pdb2gmx again to create the topol.top file with all coordinates correct:


pdb2gmx -f prot_CFY_H.pdb -o prot_complete.gro -p topol.top


(selecting amber99sb forcefield and tip3p for water, as recommended
option)

This is the message error from pdb2gmx:

Read 'FLUORESCENT
PROTEIN', 3346 atoms
Analyzing pdb file
Splitting PDB chains based on
TER records or changing chain id.
There are 1 chains and 0 blocks of
water and 218 residues with 3346 atoms

  chain #res #atoms
  1 'A' 213
3346



I'd be concerned about the difference in residue count here, but 4.5.4 is
so old I've no idea whose fault this is.



All occupancies are one
Opening force field file
./amber99sb.ff/atomtypes.atp
Atomtype 1
Reading residue database...
(amber99sb)
Opening force field file
./amber99sb.ff/aminoacids.rtp
Residue 94
Sorting it all out...
Opening
force field file ./amber99sb.ff/dna.rtp
Residue 110
Sorting it all
out...
Opening force field file ./amber99sb.ff/rna.rtp
Residue
126
Sorting it all out...
Opening force field file
./amber99sb.ff/aminoacids.hdb
Opening force field file
./amber99sb.ff/dna.hdb
Opening force field file
./amber99sb.ff/rna.hdb
Opening force field file
./amber99sb.ff/aminoacids.n.tdb
Opening force field file
./amber99sb.ff/aminoacids.c.tdb

Processing chain 1 'A' (3346 atoms, 213
residues)
There are 327 donors and 319 acceptors
There are 539 hydrogen
bonds
Will use HISE for residue 22
Will use HISD for residue 38
Will use
HISE for residue 62
Will use HISE for residue 68
Will use HISD for
residue 109
Will use HISE for residue 119
Will use HISE for residue
172
Will use HISH for residue 193
Will use HISH for residue 197
Will use
HISE for residue 217
Identified residue SER3 as a starting
terminus.
Identified residue SER218 as a ending terminus.
8 out of 8
lines of specbond.dat converted successfully
Special Atom Distance
matrix:
  MET9 MET11 MET15 HIS22 HIS38 MET41 MET47
  SD110 SD149 SD232
NE2317 NE2549 SD596 SD700
  MET11 SD149 0.807
  MET15 SD232 2.279 1.627

HIS22 NE2317 3.707 2.983 1.466
  HIS38 NE2549 1.401 0.928 2.127 3.254

MET41 SD596 1.458 0.665 1.144 2.384 1.001
  MET47 SD700 3.059 2.324 0.995
0.801 2.656 1.761
  MET53 SD777 2.786 1.999 0.990 1.171 2.160 1.373
0.603
  HIS62 NE2917 2.340 1.733 0.833 1.797 1.988 1.236 1.583
  HIS68
NE21002 0.884 0.597 1.466 2.916 1.356 0.885 2.347
  HIS109 NE21638 2.061
1.886 1.380 2.614 2.661 1.862 2.279
  HIS119 NE21803 1.459 0.967 0.923
2.372 1.617 0.812 1.870
  MET135 SD2041 3.480 2.751 1.316 0.606 2.919
2.121 0.993
  MET162 SD2439 2.521 1.976 1.656 2.412 1.855 1.543 2.264

HIS172 NE22588 3.632 2.949 1.894 1.657 2.872 2.338 1.945
  CYS174 SG2623
2.968 2.372 1.452 1.861 2.428 1.848 1.924
  MET189 SD2891 2.167 2.379
2.736 4.000 2.754 2.569 3.722
  HIS193 NE22942 2.003 2.001 2.490 3.686
2.049 2.075 3.396
  HIS197 NE23011 2.012 1.634 1.830 2.896 1.554 1.426
2.614
  HIS217 NE23329 2.545 2.376 2.831 3.805 2.039 2.305 3.575
  MET53
HIS62 HIS68 HIS109 HIS119 MET135 MET162
  SD777 NE2917 NE21002 NE21638
NE21803 SD2041 SD2439
  HIS62 NE2917 1.363
  HIS68 NE21002 2.107 1.482

HIS109 NE21638 2.365 1.568 1.372
  HIS119 NE21803 1.688 0.976 0.584
1.078
  MET135 SD2041 1.057 1.365

Re: [gmx-users] Installing GROMACS4.6.1 on Intel MIC

2013-03-21 Thread Szilárd Páll

FYI: As much as Intel likes to say that you can just run MPI/MPI+OpenMP
code on MIC, you will probably not be impressed with the performance (it
will be *much* slower than a Xeon CPU).

If you want to know why and what/when are we doing something about it,
please read my earlier comments on MIC posted to the mailing list.

--
Szilárd


On Thu, Mar 21, 2013 at 1:49 PM, Mark Abraham mark.j.abra...@gmail.comwrote:

 Yes, you can use any kind of FFTW installation for correct results.
 Hardware for which FFTW provides no SIMD acceleration will have to fall
 back on the generic FFTW routines. (Or you might consider using MKL (or
 MKL's FFTW-wrapper feature), which I'd guess Intel supports on MIC. We are
 making MKL easier to use in 4.6.2.)

 Mark

 On Wed, Mar 20, 2013 at 7:41 AM, Anirban reach.anirban.gh...@gmail.com
 wrote:

  Dear ALL,
 
  I am trying to install GROMACS4.6.1 on Intel MIC processors. A question,
  can GROMACS4.6.1 be compiled using FFTW optimization other than SSE/SSE2
  (as Intel MIC does not support SSE2 instructions)?
 
  Regards,
 
  Anirban
  --
  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 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] help with chromophore of a GFP

2013-03-21 Thread lloyd riggs

I had problems having not used gromacs in years a couple years ago.  Try 
running it through with the output as a pdb from pdb2gmx, cut off all headers, 
and you can then just compare the two files in gedit emacs or word and see 
differences.  That might help.  I routinely just keep everything in pdb format 
as its easier than jumping back and forth.


 Original-Nachricht 
 Datum: Thu, 21 Mar 2013 21:43:16 +0100
 Von: Mark Abraham mark.j.abra...@gmail.com
 An: Discussion list for GROMACS users gmx-users@gromacs.org
 Betreff: Re: [gmx-users] help with chromophore of a GFP

 On Thu, Mar 21, 2013 at 4:30 PM, Anna MARABOTTI amarabo...@unisa.it
 wrote:
 
 
 
  Dear Mark,
 
  thank you for your message. I'm happy to be on the
  right track; unfortunately the end point seems to be very far away...
 
 
  I tried to obtain that CFY hydrogens and protein hydrogens are all
  matching the aminoacids.rtp entry, in order to avoid dealing with
  aminoacids.hdb. This is what I did:
 
  - starting from the pdb file of
  the protein, I removed CFY entry (prot_noCFY.pdb)
 
  - I used pdb2gmx to
  add H to the protein only: pdb2gmx -f prot_noCFY.pdb -o prot_noCFY_H.pdb
  -p topol.top
 
  - I inserted CFY_H.pdb (obtained with Pymol in a previous
  passage in which I added H with Pymol to the protein, including CFY)
  into prot_noCFY_H.pdb, obtaining prot_CFY_H.pdb.
 
  In this way, H atoms
  bound to regular residues have been added using Amber99SB, therefore
  they are compatible with this ff, and atoms of CFY (previously added
  with Pymol) have the same naming convention in aminoacids.rtp (that I
  edited using atom types, charges etc. calculated with Antechamber on
  this molecule coming from Pymol). Obviously, the atom numbering is not
  sequential: the last atom of V63 (the last regular residue before CFY)
  is numbered 938, the first atom of H68 (the first regular residue
  after CFY) is numbered 939, and the atoms of CFY66 are numbered from 1
  to 70. Moreover, since the sequence of atoms in aminoacids.rtp is not
  the same as in the coordinates of CFY (I adapted the sequence of atoms
  following the format of other residues in aminoacids.rtp), the numbering
  of CFY in the prot_CFY_H.pdb is not ordered (1-2-3--69-70) but
  disordered (19-54-20-55...49-50-24-25).
 
 
 Seems fine. pdb2gmx is mostly about atom/residue naming. grompp is mostly
 about atom/residue/moleculetype ordering.
 
 - At this stage, I used
  pdb2gmx again to create the topol.top file with all coordinates correct:
 
 
  pdb2gmx -f prot_CFY_H.pdb -o prot_complete.gro -p topol.top
 
 
  (selecting amber99sb forcefield and tip3p for water, as recommended
  option)
 
  This is the message error from pdb2gmx:
 
  Read 'FLUORESCENT
  PROTEIN', 3346 atoms
  Analyzing pdb file
  Splitting PDB chains based on
  TER records or changing chain id.
  There are 1 chains and 0 blocks of
  water and 218 residues with 3346 atoms
 
   chain #res #atoms
   1 'A' 213
  3346
 
 
 I'd be concerned about the difference in residue count here, but 4.5.4 is
 so old I've no idea whose fault this is.
 
 
  All occupancies are one
  Opening force field file
  ./amber99sb.ff/atomtypes.atp
  Atomtype 1
  Reading residue database...
  (amber99sb)
  Opening force field file
  ./amber99sb.ff/aminoacids.rtp
  Residue 94
  Sorting it all out...
  Opening
  force field file ./amber99sb.ff/dna.rtp
  Residue 110
  Sorting it all
  out...
  Opening force field file ./amber99sb.ff/rna.rtp
  Residue
  126
  Sorting it all out...
  Opening force field file
  ./amber99sb.ff/aminoacids.hdb
  Opening force field file
  ./amber99sb.ff/dna.hdb
  Opening force field file
  ./amber99sb.ff/rna.hdb
  Opening force field file
  ./amber99sb.ff/aminoacids.n.tdb
  Opening force field file
  ./amber99sb.ff/aminoacids.c.tdb
 
  Processing chain 1 'A' (3346 atoms, 213
  residues)
  There are 327 donors and 319 acceptors
  There are 539 hydrogen
  bonds
  Will use HISE for residue 22
  Will use HISD for residue 38
  Will use
  HISE for residue 62
  Will use HISE for residue 68
  Will use HISD for
  residue 109
  Will use HISE for residue 119
  Will use HISE for residue
  172
  Will use HISH for residue 193
  Will use HISH for residue 197
  Will use
  HISE for residue 217
  Identified residue SER3 as a starting
  terminus.
  Identified residue SER218 as a ending terminus.
  8 out of 8
  lines of specbond.dat converted successfully
  Special Atom Distance
  matrix:
   MET9 MET11 MET15 HIS22 HIS38 MET41 MET47
   SD110 SD149 SD232
  NE2317 NE2549 SD596 SD700
   MET11 SD149 0.807
   MET15 SD232 2.279 1.627
 
  HIS22 NE2317 3.707 2.983 1.466
   HIS38 NE2549 1.401 0.928 2.127 3.254
 
  MET41 SD596 1.458 0.665 1.144 2.384 1.001
   MET47 SD700 3.059 2.324 0.995
  0.801 2.656 1.761
   MET53 SD777 2.786 1.999 0.990 1.171 2.160 1.373
  0.603
   HIS62 NE2917 2.340 1.733 0.833 1.797 1.988 1.236 1.583
   HIS68
  NE21002 0.884 0.597 1.466 2.916 1.356 0.885 2.347
   HIS109 NE21638 2.061
  1.886 1.380

Re: [gmx-users] cuda gpu status on mdrun

2013-03-21 Thread Szilárd Páll

Hi Quentin,

That's just a way of saying that something is wrong with either of the
following (in order of possibility of the event):
- your GPU driver is too old, hence incompatible with your CUDA version;
- your GPU driver installation is broken;
- your GPU is behaving in an unexpected/strange manner.

Note that GF 8400 is way too old and therefore incompatible with GROMACS,
you'll need at least a compute capability 2.0 card.

Cheers,

--
Szilárd

On Tue, Mar 19, 2013 at 12:53 AM, Quentin Delettre
quentin.delet...@gmail.com wrote:

Hi,

I am new to gromacs and started playing a bit on my laptop (Lenovo Y510,
Geforce 8400M GT) running ubuntu 12.10 with cuda 5.0.

Everything is working well, gromacs does not complain about anything. But
sometimes when using mdrun at start the gpu status is insane. What does
that mean ?

Thank you.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Searchhttp://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_Listshttp://www.gromacs.org/Support/Mailing_Lists

[gmx-users] interaction with metal

2013-03-21 Thread Nur Syafiqah Abdul Ghani

Hi guys,

I have a question..Regarding to my project,i want to make a simulation
between metal and my protein in mix solvent condition.

BUt for gromacs,at the genion part can i run it for two times?
First to make my simulation system is neutral and the second one is to
use the genion to put the metal and interact it with my protein.Is it
possible to do that?

--
Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
alternative email : syafiqahabdulgh...@gmail.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] interaction with metal




On 3/21/13 8:59 PM, Nur Syafiqah Abdul Ghani wrote:

Hi guys,

I have a question..Regarding to my project,i want to make a simulation
between metal and my protein in mix solvent condition.

BUt for gromacs,at the genion part can i run it for two times?
First to make my simulation system is neutral and the second one is to
use the genion to put the metal and interact it with my protein.Is it
possible to do that?



genion only inserts ions randomly, so if you need to specify a particular 
location for your metal ion, you're better off simply setting its coordinates 
with e.g. editconf and placing it in your box, then adding solvent and whatever 
other ions you need.


-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] proper and improper dihedrals in topology file from other ff

2013-03-21 Thread 라지브간디

Dear gmx users,


I am MD simulation for heme ligated protein where i given all bond and angle, 
dihedral information in topology file created by pd2gmx ( gromos43a1).


However, i do not know how to interpret the proper and improper dihedrals in 
topology file? I have looked over the .rtp file and found that gromos mentioned 
like
 
example:


[ impropers ]
;  aiajakal   gromos type
   C2N1N3   NA2 gi_1
  NA2  HA21  HA22C2 gi_1
   N3C2C4   HA3 gi_1   


But the the parameter  I use from literature where its in charmm and amber 
format as they mentioned the torsions like following way.


Improper 
CPB-X-X-CR1E90.0   0.0 
CC - X-X-NB   18.3 0.0   


...etc


How do i use this improper to utilize in gromos? 


Thanks in advance.
-- 
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] proper and improper dihedrals in topology file from other ff




On 3/21/13 10:20 PM, 라지브간디 wrote:

Dear gmx users,


I am MD simulation for heme ligated protein where i given all bond and angle, 
dihedral information in topology file created by pd2gmx ( gromos43a1).


However, i do not know how to interpret the proper and improper dihedrals in 
topology file? I have looked over the .rtp file and found that gromos mentioned 
like

example:


[ impropers ]
;  aiajakal   gromos type
C2N1N3   NA2 gi_1
   NA2  HA21  HA22C2 gi_1
N3C2C4   HA3 gi_1


But the the parameter  I use from literature where its in charmm and amber 
format as they mentioned the torsions like following way.


Improper
CPB-X-X-CR1E90.0   0.0
CC - X-X-NB   18.3 0.0


...etc


How do i use this improper to utilize in gromos?



Every force field has small differences in format.  Look at ffbonded.itp for 
43A1 and you will see #define statements that correspond to bonds (gb_*), angles 
(ga_*), etc.  Those macros just mean substitute this information here.  It's 
shorthand.  So either you can introduce a new definition in ffbonded.itp or just 
type the parameters in manually according to the format specified in the manual.


-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] construct the long polymer chain

2013-03-21 Thread cqgzc

Hi
I have been following
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html(procedure
by Justin) to construct the Polyethylene (PE). However, I can only get the
PE with length 6 just like
CH3-CH2-CH2-CH2-CH2-CH3. Therefore, I want to know how to obtain the long
polymer chain(e.g. length=20) using this method. Any help with my
appreciate.



--
View this message in context: 
http://gromacs.5086.n6.nabble.com/construct-the-long-polymer-chain-tp5006547.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] construct the long polymer chain