[gmx-users] ambconv problems

[david.evans at ulsop.ac.uk]

Dear all,

I'm a new GROMACS user, and I'd like to use the contributed AMBCONV utility, but am having some problems.

The first are caused by the change of format of the AMBER .atop file, which one can solve quite easily by saving an old format file from Leap, and deleting the last (seventh) parameter from the fourth line.

More seriously, there seem to be issues with the memory management, as the atop->numbnd value seems to be getting corrupted between input and it being used, resulting in failure. I tried to work around this, but have as yet been unable to produce .top and .itp files that GROMACS is happy with.

Is anyone out there using AMBCONV regularly? I understand that it is not part of the supported distribution, but if the original author or any other experienced users could help me out I'd be very grateful. I'm very interested in being able to use GROMACS as a replacement for sander, while still using the AMBER potentials and utilities for setting up my system.

I'm using gcc-3.2.2 on RedHat9, if that has any relevance. I'd like to convert .atop and .rst files produced by Leap from AMBER7 and/or AMBER8.

Thanks

David Evans
London School of Pharmacy

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