Hi,
Two points:
1) Who says that there is anything wrong? The message (a warning, not an
error message) says that assigned bond types *may* be wrong. It is up to
you to check if this is the case or not - so first check if the bond types
are what you'd expect for aspartic acid / glutamic acid.
2) Do you have a special reason to try and generate parameters for "all
[your] proteins" with antechamber? If you are trying to do a normal MD
simulation, you should pick a force field designed (& validated) for
proteins, not go through antechamber to generate GAFF parameters.
--Marc
On 28 May 2012 07:58, ashley chen <ashley.huijia15.gmail.com> wrote:
> Hi there,
>
> I am using Antechamber for generating my prep file using the charges from a
> gaussian output file.
>
> I want to fit it using RESP.
>
> For all my proteins it is working fine. But for residues with aspartic acid
> and glutamic acid it gives me the following error.
>
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase PSCUTOFF in define.h and recompile bondtype.c
> Be cautious, use a large value of PSCUTOFF (>100) will significantly
> increase the computation time
>
> when the follow antechamber command is used:
> antechamber -i mol.log –fi gout –o mol.mol2 –fo mol2 –c resp
>
> Can anyone advise me on how to solve this problem? Thank you.
>
> Regards,
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>
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Received on Mon May 28 2012 - 01:00:02 PDT
