[gmx-users] OPLS, pdb2gmx and hydrogen nomenclature

Sandeep Somani ssomani at bii.a-star.edu.sg
Tue Jun 21 12:33:29 CEST 2005 

Hi 
    As you mentioned I had listed the entries i made to all the
parameter files ( ffoplsaa.atp ffoplsaa.rtp ffoplsaanb.itp ffoplsaa.hdb
ffoplsaabon.itp ) in my mail. i know the mail was too long! 
 
basically my question was -- 
        is there is any convention to be followed for naming hydrogens
in any new molecule ?  
 
-sandeep
 
 

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of ÎâÏÔ»Ô
Sent: Tuesday, June 21, 2005 4:17 PM
To: Discussion list for GROMACS user
Subject: Re: [gmx-users] OPLS, pdb2gmx and hydrogen nomenclature


You should create a new force field parameter for your molecule in the
ffoplsaa.rtp. In this file, you can create the parameters basing on the
amino acid residues. The bonded and non-bonded parameters can be got
from the ffoplsaa.itp and ffoplsaanb.itp..Good luck!
 
 
  _____  

Hi
 
I was trying to construct an OPLS topology for benzene by using PHE
residue parameters.
 
I made local copies of ffopls* files and deleted everything except
entries related to my residue (listed at the end).
 
My pdb files looks like (note first two lines):
 
ATOM      1  CG  BEN     1      42.710  25.370  54.530  1.00  0.000
ATOM      2  HG1 BEN     1      42.610  26.860  54.540  1.00  0.000
ATOM      3  CD1 BEN     1      43.930  24.740  54.620  1.00  0.000
ATOM      4  HD1 BEN     1      44.770  25.280  54.700  1.00  0.000
ATOM      5  CD2 BEN     1      41.570  24.590  54.430  1.00  0.000
ATOM      6  HD2 BEN     1      40.670  25.040  54.380  1.00  0.000
ATOM      7  CE1 BEN     1      44.030  23.350  54.600  1.00  0.000
ATOM      8  HE1 BEN     1      44.930  22.910  54.670  1.00  0.000
ATOM      9  CE2 BEN     1      41.650  23.210  54.400  1.00  0.000
ATOM     10  HE2 BEN     1      40.810  22.670  54.330  1.00  0.000
ATOM     11  CZ  BEN     1      42.880  22.590  54.480  1.00  0.000
ATOM     12  HZ  BEN     1      42.940  21.590  54.460  1.00  0.000
 
Now
  pdb2gmx -f mypdb.pdb -missing
results in topol.top:
[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB
     1   opls_145      1    BEN     CG      1     -0.115     12.011
     2   opls_146      1    BEN     HG      1      0.115      1.008
     3   opls_146      1    BEN    HG1      1      0.115      1.008
...
 
My question is:
Where has atom HG come from ?! it is not in any of the parameter files.
 
but with the -ignh flag HG1 is removed while HG is generated.
 
does pdb2gmx have a constraint on the nomenclature of hydrogens ?
 
Thnx in advance ..
sandeep
 
*************************************************
Parameter file listing -
 
ffoplsaa.atp
------------
 
 opls_145   12.01100  ;
 opls_146    1.00800  ; Benzene H - 12 site.
 
ffoplsaa.rtp
------------
[ BEN ]
 [ atoms ]
    CG    opls_145   -0.115     2
   HG1    opls_146    0.115     2   ; < 
-- NOTE: HG1, not HG
   CD1    opls_145   -0.115     3
   HD1    opls_146    0.115     3
   CD2    opls_145   -0.115     4
   HD2    opls_146    0.115     4
   CE1    opls_145   -0.115     5
   HE1    opls_146    0.115     5
   CE2    opls_145   -0.115     6
   HE2    opls_146    0.115     6
    CZ    opls_145   -0.115     7
    HZ    opls_146    0.115     7
 [ bonds ]
    CG    HG1
    CG    CD1
    CG    CD2
   CD1   HD1
   CD1   CE1
   CD2   HD2
   CD2   CE2
   CE1   HE1
   CE1    CZ
   CE2   HE2
   CE2    CZ
    CZ    HZ
 [ impropers ]
    CG    CE2   CD2   HD2    improper_Z_CA_X_Y
   CD2    CZ   CE2   HE2    improper_Z_CA_X_Y
   CE1   CE2    CZ    HZ    improper_Z_CA_X_Y
   CD1    CZ   CE1   HE1    improper_Z_CA_X_Y
    CG    CE1   CD1   HD1    improper_Z_CA_X_Y
   CD1   CD2    CG    HG1     improper_Z_CA_X_Y
 
ffoplsaanb.itp
--------------
[ atomtypes ]
; name  bond_type    mass    charge   ptype          sigma      epsilon
 opls_145   CA     12.01100    -0.115       A    3.55000e-01
2.92880e-01
opls_146   HA      1.00800     0.115       A    2.42000e-01  1.25520e-01
 
ffoplsaa.hdb
------------
BEN  6
1 1 CG  CD1     CD2
1 1 CD1 CG  CE1
1 1 CD2 CG  CE2
1 1 CE1 CD1 CZ
1 1 CE2 CD2 CZ
1 1 CZ CE1 CE2
 
 
ffoplsaabon.itp
---------------
[ bondtypes ]
; i    j  func       b0          kb
  CA    CA      1    0.14000   392459.2   ; TRP,TYR,PHE
  CA    HA      1    0.10800   307105.6   ; PHE, etc.
 
[ angletypes ]
;  i    j    k  func       th0       cth
  CA     CA     CA      1   120.000    527.184   ; PHE(OL)
  CA     CA     HA      1   120.000    292.880   ;
 
[ dihedraltypes ]
;  i    j    k    l   func     coefficients
  X      CA     CA     X       3     30.33400   0.00000 -30.33400
0.00000   0.00000   0.00000 ; aromatic ring
 
[ dihedraltypes ]
; Z -CA-X -Y improper torsion. CA is any ring carbon
(CA,CB,CN,CV,CW,CR,CK,CQ,CS,C*)
#define improper_Z_CA_X_Y       180.0      4.60240   2
 
 
 
 
 
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