Re: [gmx-users] gold-S simulation

2012-12-19 Thread Justin Lemkul



On 12/19/12 6:02 AM, fatemeh ramezani wrote:

Dear Justin

I want exactly this, that the distance between Au-S be stable around 
equilibrium value, For this purpose,Should I put the harmonic parameters 
related to the  gold and sulfur  in ffbonded file? Or I should consider AU-S 
connection as VonderWaals and put its epsilon and sidma in ffnonbonded file?



Please be mindful to only parse the relevant portion of the digest and to use a 
real subject line.


Yes, if you want there to be a covalent bond, you need to introduce one.  Hoping 
that van der Waals parameters will hold the elements of the system in place does 
not sound like a robust approach to me.


-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


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Re: [gmx-users] gold-S simulation

2012-12-16 Thread fatemeh ramezani


Dear francesco 
I extract gold parameter from papers that I attached them for you. But  for 
gold and other atom parameters, you should calculate them using common 
combination rule. 


Fatemeh Ramezani



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Re: [gmx-users] gold-S simulation

2012-12-16 Thread fatemeh ramezani


hi 
thanks for your attention,
all itp files are in OPLSAA forcefield folder that I attached it for you. 


 
Fatemeh Ramezani




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Re: [gmx-users] gold-S simulation

2012-12-16 Thread francesco oteri
Hi fatemeh,
thank you for the references. Regarding your problem, what does it means
you don't see any interaction?
Is it possible it is just a problem of the visualization software. To be
sure, you could monitor the distance
between any S atom and the Au atom to which it is supposed to be bound. If
the distance is stable around
the equilibrium value you can say that the interaction is still present

Francesco


2012/12/16 fatemeh ramezani fr_...@yahoo.com



 hi
 thanks for your attention,
 all itp files are in OPLSAA forcefield folder that I attached it for you.



 Fatemeh Ramezani


 

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Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] gold-S simulation

2012-12-16 Thread Justin Lemkul



On 12/16/12 1:11 PM, francesco oteri wrote:

Hi fatemeh,
thank you for the references. Regarding your problem, what does it means
you don't see any interaction?
Is it possible it is just a problem of the visualization software. To be
sure, you could monitor the distance
between any S atom and the Au atom to which it is supposed to be bound. If
the distance is stable around
the equilibrium value you can say that the interaction is still present



In addition, if one is expecting some sort of covalent association, it must be 
defined in the topology.  This will not be true in the case of protein-Au 
interactions unless one makes appropriate entries in specbond.dat, similar to 
heme, or manual addition.  Bonded parameters are useless unless there is a bond :)


-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


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Re: [gmx-users] gold-S simulation

2012-12-15 Thread Peter C. Lai
Where is the .itp file for the system?

On 2012-12-15 01:40:27PM -0800, fatemeh ramezani wrote:
 hi 
 
 
 I'm simulating gold atom interaction with  aminoacidcys. I have made 
 gold-cys.pdb by hyperchem software:
 
 HETATM    1  N   CYS 1   0.000   1.335   0.000
 HETATM    2  CA  CYS 1  -0.683   1.818  -1.183
 HETATM    3  C   CYS 1  -0.705   3.339  -1.221
 HETATM    4  O   CYS 1  -0.184   3.993  -0.319
 HETATM    5  CB  CYS 1  -2.127   1.330  -1.221
 HETATM    6  SG  CYS 1  -3.106   1.859  -2.649
 HETATM    8 AU   AU  8  -2.833   0.428  -1.793
 HETATM    9 AU   AU  9  -2.647   0.381  -2.869
 HETATM   10 AU   AU 10  -1.691   1.360  -3.093
 HETATM   11 AU   AU 11  -0.647   2.706  -2.135
 HETATM   12 AU   AU 12  -2.742   0.834  -0.456
 HETATM   13 AU   AU 13  -1.691   2.061  -0.043
 HETATM   14 AU   AU 14  -0.783   3.136   0.376
 HETATM   15 AU   AU 15   0.095   3.750  -1.068
 HETATM   16 AU   AU 16  -2.929   2.480  -2.204
 HETATM   17 AU   AU 17  -3.285   1.594  -3.328
 HETATM   18 AU   AU 18  -2.544   2.593  -3.763
 HETATM   19 AU   AU 19  -1.951   1.260  -2.303
 CONECT    1    2
 CONECT    0    1
 CONECT    2    1    3    5
 CONECT    0    2
 CONECT    3    2    4
 CONECT    4    3
 CONECT    5    2    6
 CONECT    0    5
 CONECT    0    5
 CONECT    6    5
 CONECT    0    6
 CONECT    0    6
 CONECT    0    6
 END
 
  
 
 I started simulation by this pdb file. I'm using OPLSAA force field and also 
 I added gold parameter in ffnonbonded.itp  :
 .
 .
 .
 ; Added by DvdS 05/2005 copied from GROMACS force field.   
  SI SI 14    28.08000 0.000    A    3.38550e-01  
 2.44704e+00
  AU AU 79   196.9700 0.000   A    0.29510e+00  22.1120e+00
 
 [ nonbond_params ]
 AU  AU   1    0.0e+00  0.0e+00
 
 
 ; SC 08/2007: Special Au-N vdw to simulate chemical bond between 
 gold-imidazole
  AU opls_511 1    3.07000e-01  3.96000e+00
  
 ; SC 05/2008: special Au-C and Au-H to simulate pi-systems alkenes+benzene 
 (and PHE)
  AU opls_142 1    3.21000e-1   2.65400e+00
  AU opls_143 1    3.21000e-1   2.65400e+00
  AU opls_144 1    2.67000e-1   1.66500e+00
  AU opls_145 1    3.2e-1   2.54600e+00
  AU opls_146 1    2.67000e-1   1.66500e+00
  AU opls_150 1    3.21000e-1   2.65400e+00
  
 ; +imidazole and His
  AU opls_506 1    3.21000e-1   2.54000e+00
  AU opls_507 1    3.21000e-1   2.54000e+00
  AU opls_508 1    3.21000e-1   2.54000e+00
 
 ; +HisH
  AU opls_509 1    3.21000e-1   2.54000e+00
  AU opls_510 1    3.21000e-1   2.54000e+00
 ; +TYR
  AU opls_166 1    3.21000e-1   2.54000e+00
 ; +TRP
  AU opls_500 1    3.21000e-1   2.54000e+00
  AU opls_514 1    3.21000e-1   2.54000e+00
  AU opls_501 1    3.21000e-1   2.54000e+00
  AU opls_502 1    3.55000e-1   3.55000e+00
 
 and I concidered AU-S as bonding connection and I added its parameter (bond 
 stretch, dihedral and angle ) in ffbonded.itp file: 
 [ bondtypes ]
 ; i    j  func   b0  kb
 .
 .
 .
 AU    SH  1    0.24000   165528.0   ;
 AU    S   1    0.24000   165528.0   ;
 AU    SG  1    0.24000   165528.0   ;
 .
 .
 .
 [ angletypes ]
 ;  i    j    k  func   th0   cth
 .
 .
 .
   AU SG CB  1   109.00 46.34
   AU SH CB  1   109.00 46.34
   AU S  CB  1   109.00 46.34
 .
 .
 .
 [ dihedraltypes ]
 .
 .
 .
 #define improper_AU_S_CB_CA    -180.0  1.2958 2 
 
 #define improper_AU_SH_CB_CA   -180.0  1.2958 2
 
 #define improper_AU_SG_CB_CA    -180   1.2958 2
 
 #define improper_AU_S_C_C 19   0.9196 2
 
 #define improper_AU_SH_C_C    19   0.9196 2
 
 #define improper_AU_SG_C_C    19   0.9196 2
 .
 .
 .
 
 when I run my simulation I dont see any interaction or affinity between gold 
 atom and S atom of cystein, while it is clear that gold shoud has interaction 
 with sulfur. what is its reason? I'm completely confused. I tried anythings 
 that I can but my system doesn't work.
 
 please help me
  
 
 Fatemeh Ramezani
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Re: [gmx-users] gold-S simulation

2012-12-15 Thread francesco oteri
Hi fatemeh,
I am looking for prameters like yours, where have you took the parameters
for gold and gold-aminoacid inteaction?

Francesco


2012/12/16 Peter C. Lai p...@uab.edu

 Where is the .itp file for the system?

 On 2012-12-15 01:40:27PM -0800, fatemeh ramezani wrote:
  hi
 
 
  I'm simulating gold atom interaction with  aminoacidcys. I have made
 gold-cys.pdb by hyperchem software:
 
  HETATM1  N   CYS 1   0.000   1.335   0.000
  HETATM2  CA  CYS 1  -0.683   1.818  -1.183
  HETATM3  C   CYS 1  -0.705   3.339  -1.221
  HETATM4  O   CYS 1  -0.184   3.993  -0.319
  HETATM5  CB  CYS 1  -2.127   1.330  -1.221
  HETATM6  SG  CYS 1  -3.106   1.859  -2.649
  HETATM8 AU   AU  8  -2.833   0.428  -1.793
  HETATM9 AU   AU  9  -2.647   0.381  -2.869
  HETATM   10 AU   AU 10  -1.691   1.360  -3.093
  HETATM   11 AU   AU 11  -0.647   2.706  -2.135
  HETATM   12 AU   AU 12  -2.742   0.834  -0.456
  HETATM   13 AU   AU 13  -1.691   2.061  -0.043
  HETATM   14 AU   AU 14  -0.783   3.136   0.376
  HETATM   15 AU   AU 15   0.095   3.750  -1.068
  HETATM   16 AU   AU 16  -2.929   2.480  -2.204
  HETATM   17 AU   AU 17  -3.285   1.594  -3.328
  HETATM   18 AU   AU 18  -2.544   2.593  -3.763
  HETATM   19 AU   AU 19  -1.951   1.260  -2.303
  CONECT12
  CONECT01
  CONECT2135
  CONECT02
  CONECT324
  CONECT43
  CONECT526
  CONECT05
  CONECT05
  CONECT65
  CONECT06
  CONECT06
  CONECT06
  END
 
 
 
  I started simulation by this pdb file. I'm using OPLSAA force field and
 also I added gold parameter in ffnonbonded.itp  :
  .
  .
  .
  ; Added by DvdS 05/2005 copied from GROMACS force field.
   SI SI 1428.08000 0.000A3.38550e-01
 2.44704e+00
   AU AU 79   196.9700 0.000   A0.29510e+00
 22.1120e+00
 
  [ nonbond_params ]
  AU  AU   10.0e+00
 0.0e+00
 
 
  ; SC 08/2007: Special Au-N vdw to simulate chemical bond between
 gold-imidazole
   AU opls_511 13.07000e-01
 3.96000e+00
 
  ; SC 05/2008: special Au-C and Au-H to simulate pi-systems
 alkenes+benzene (and PHE)
   AU opls_142 13.21000e-1
 2.65400e+00
   AU opls_143 13.21000e-1
 2.65400e+00
   AU opls_144 12.67000e-1
 1.66500e+00
   AU opls_145 13.2e-1
 2.54600e+00
   AU opls_146 12.67000e-1
 1.66500e+00
   AU opls_150 13.21000e-1
 2.65400e+00
 
  ; +imidazole and His
   AU opls_506 13.21000e-1
 2.54000e+00
   AU opls_507 13.21000e-1
 2.54000e+00
   AU opls_508 13.21000e-1
 2.54000e+00
 
  ; +HisH
   AU opls_509 13.21000e-1
 2.54000e+00
   AU opls_510 13.21000e-1
 2.54000e+00
  ; +TYR
   AU opls_166 13.21000e-1
 2.54000e+00
  ; +TRP
   AU opls_500 13.21000e-1
 2.54000e+00
   AU opls_514 13.21000e-1
 2.54000e+00
   AU opls_501 13.21000e-1
 2.54000e+00
   AU opls_502 13.55000e-1
 3.55000e+00
 
  and I concidered AU-S as bonding connection and I added its parameter
 (bond stretch, dihedral and angle ) in ffbonded.itp file:
  [ bondtypes ]
  ; ij  func   b0  kb
  .
  .
  .
  AUSH  10.24000   165528.0   ;
  AUS   10.24000   165528.0   ;
  AUSG  10.24000   165528.0   ;
  .
  .
  .
  [ angletypes ]
  ;  ijk  func   th0   cth
  .
  .
  .
AU SG CB  1   109.00 46.34
AU SH CB  1   109.00 46.34
AU S  CB  1   109.00 46.34
  .
  .
  .
  [ dihedraltypes ]
  .
  .
  .
  #define improper_AU_S_CB_CA-180.0  1.2958 2
 
  #define improper_AU_SH_CB_CA   -180.0  1.2958 2
 
  #define improper_AU_SG_CB_CA-180   1.2958 2
 
  #define improper_AU_S_C_C 19   0.9196 2
 
  #define improper_AU_SH_C_C19   0.9196 2
 
  #define improper_AU_SG_C_C19   0.9196 2
  .
  .
  .
 
  when I run my simulation I dont see any interaction or affinity between
 gold atom and S atom of cystein, while it is clear that gold shoud has
 interaction with sulfur. what is its reason? I'm completely confused. I
 tried anythings that I can but my system doesn't