[gmx-users] problem with the amb2gmx.pl

xiao helitrope at 126.com
Wed Oct 9 15:07:16 CEST 2013

Dear all,
I am doing membrane protein simulation by using amber force field. The lipid force field parameters are from the lipid11.dat from Amber. Firstly, i got the xx.prmtop and xx.prmcrd files, and then i used amb2gmx.pl to convert the xx.prmtop and xx.prmcrd files into gromacs files xx.top and xx.gro files. However, i found there is some problem with the xx.top files.  For example, there are two dihedral parameters, and they should be same, but in the xx.top file (gromacs form) ,they are different. I have no idea where the problem is from.
Any information is appreciated!

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