[gmx-users] amber convert gromacs input files

[Oliver Grant]

Hi,

Not sure exactly what you plan to simulate but here are a couple of
potential pitfalls:

Does acpype call amb2gmx.pl or is it new code that converts? If it is a
amb2gmx.pl call I'd check the torsions on the NAc group if you have one.
They didn't get translated when I used it.

When using amber ports be careful about using default index groups like
"protein" or "C alpha" as they won't contain atoms from residues like LYP
that are different in the ports.

Also you'll want to set fudge to 1.0 in the amber99sb.itp  or where it is
set (can't check this atm) if simulating the sugar alone. Its due to
differences in the way amber and glycam are parametrized. (If you are
interested it is differences in 1-4 scaling).

There may be other issues I'm not aware of yet. :)

All the best,
Oliver

On 23 December 2010 18:13, Alan Wilter Sousa da Silva <awilter at ebi.ac.uk>wrote:

> Have a look at acpype.googlecode.com
>
> Alan
>
> 2010/12/23 gromacs564 <gromacs564 at 126.com>
>
>>
>> Hi ,
>>
>>      I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam web(they are glycam06 force field,included in AMBER) ,  but cannot  converted this amber files to gromacs files format.
>>
>>
>>      Can anyone help me to convert this (amber) files to gromacs input files(top or itp,gro).?
>>
>> Many thanks!
>>
>>
>>
>>
>>
>>
>>
>>
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>
>
>
> --
> Alan Wilter SOUSA da SILVA, D.Sc.
> Bioinformatician, UniProt - PANDA, EBI-EMBL
> CB10 1SD, Hinxton, Cambridge, UK
> +44 1223 49 4588
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>
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