[gmx-users] Re: Regarding POPE " H " atom type modification

[naga raju]

Dear gmx users,
                
        Dear Dr.Oliver as per your suggestion, I did
the modification of H atom type for POPE  lipid
molecule. Here I am giving what I have done
modification in ffoplsaanb.itp file under [ atomtype ]
section.
(1) First I tried as given below
    
 opls_963   CT     6     12.01100     0.120       A   
3.50000e-01  2.76144e-01
 opls_964   CT     6     12.01100     0.480       A   
3.50000e-01  4.05848e-01
 opls_965   F      9     18.99840    -0.120       A   
2.95000e-01  2.21752e-01
  H   H   1    1.00800     0.400       A   
0.00000e+00  0.00000e+00

(2) Second I tried as given below ( "H" atom type was
added after lipid atom types) 

 LC3     15.035     0     A     3.96E-01     6.06E-01
 LC2     14.027     0     A     3.80E-01     4.94E-01
   H      1.008     0     A     0.000e+00    0.000e+00

In both the cases i got the error as show below.
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 2095.427979 (between atoms 4422 and 4424) rms
69.822533
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint
length
      1      4   90.0    0.1000   3.5921      0.1000
      2      4   90.0    0.1000  29.8166      0.1000
      3      4   90.0    0.1000   3.4683      0.1000
      4      5   90.0    0.1470   3.7039      0.1470
      5      6   67.6    0.1530   0.1440      0.1530
      6      7   90.2    0.1430   1.8286      0.1430
      7      8   90.0    0.1610   1.2737      0.1610
....................
...................
...................
after some time segmentation fault
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx\
Could you suggest me where I have done mistake.

I have one more question regardsing POPE "H" atom
type.
In the mailing list
http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html
given that "H" atom type belongs to opls_369. But when
I observed in ffoplsaa.atp file it is belongs to
Guanine H-NC2. 
My question is, 
            In POPE lipid "H" atom type (NH3-C-C-), is
it not belongs to opls_105    1.00800  ; H (RNH3+)
type?

In case of POPG lipid molecule,
                                For glycerol "O" "H"
atom types, may i take opls_171 and opls_172
paramters?

Any suggestion is appreciated.
                      Thank you in advance.
                                             

                       with regards,
                         Nagaraju



 
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