Dear gmx users,
I want to simulate popc in water. What I have done is:
1.Build the popc.top file using the popc.itp parameters and including gmx.ff,
lipid.itp and spce.itp in it as below;
; Include forcefield parameters
#include "./gmx.ff/forcefield.itp"
; Include water topology
#include "./gmx.ff/spce.itp"
#include "lipid.itp"
[ moleculetype ]
; Name nrexcl
POPC 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 LC3 1 POP C1 0 0.4000 15.0350 ;
qtot:0.36
2 LC3 1 POP C2 0 0.4000 15.0350 ;
qtot:0.72
.
.
.
[ bonds ]
; ai aj funct
4 5 1 0.14700E+00 0.37660E+06
5 6 1 0.15300E+00 0.33470E+06
6 7 1 0.14300E+00 0.25100E+06
.
.
.
[ pairs ]
; ai aj funct
1 6 1
2 6 1
.
.
.
[ angles ]
; ai aj ak funct
4 5 6 1 0.10950E+03 0.46020E+03
5 6 7 1 0.10950E+03 0.46020E+03
6 7 8 1 0.12000E+03 0.39750E+03
7 8 9 1 0.10960E+03 0.39750E+03
48 49 50 1 0.11100E+03 0.46020E+03
1 4 2 1 0.10950E+03 0.33470E+03
2 4 3 1 0.10950E+03 0.33470E+03
3 4 1 1 0.10950E+03 0.33470E+03
1 4 5 1 0.10950E+03 0.37660E+03
2 4 5 1 0.10950E+03 0.37660E+03
3 4 5 1 0.10950E+03 0.37660E+03
[ dihedrals ]
; ai aj ak al funct phi0 cp mult
1 4 5 6 1 0.0 3.76 3
4 5 6 7 1 0.0 5.85 3
.
.
.
[ dihedrals ]
; ai aj ak al funct
13 14 32 12 2 35.264 0.33470E+03
15 14 17 16 2 0.00000E+00 0.16740E+03
34 33 36 35 2 0.00000E+00 0.16740E+03
23 24 25 26 2 0.000 167.360
[ system ]
; name
POPC in water
[ molecules ]
; name number
POPC 128
SOL 3802
But I still get the "fatal error : Atomtype LC3 not found ".
What is the problem? Anybody may help me please?
Thanks in advance,
Shima
--
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
