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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