[gmx-users] AMP_simulation

[niki24 at tezu.ernet.in]

Hello,

I have tried doing the Molecular dynamics simulation of AMP using the
Gromos54a7 forcefield.

ITP parameters for the AMP molecule has been generated using the ATB
builder. Minimization of the molecule goes on well however while carrying
out the Nvt theres a segmantation fault resulting in step files.

Moreover LINCS warning are shown with bonds that rotated more than 30
degrees. ihave tried changing lincs parameter and also increasing the step
size, but still simulation crashes.

Is it suggestible to generate topology for the AMP molecule from the
available topological parameters of ATP in GROMACS. Or are their any
source of getting the correct itp paremeters for "AMP".

Thanks
Nikita Bora


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