[gmx-users] amber ports in gromas - bond length warning

[Yang Ye]

What are the atoms involved in the Long Bond waring?

For cyclic peptide, you also need to hand edit the topology file after 
pdb2gmx to connect the last residue to the first residue.

Regards,
Yang Ye

David van der Spoel wrote:
> N-J.M. Macaluso wrote:
>> Hello,
>>
>> I am using the Amber ports for Gromacs provided by the following 
>> website: http://chemistry.csulb.edu/ffamber/
>>
>> I would like to use the Amber99sb force field for the simulation of a 
>> cyclic peptide, joined by a disulfide bond between terminal cysteine 
>> residues. I think I am using the appropriate Amber residue notation 
>> in the pdb file for each cysteine. The N-terminal cysteine is called 
>> NCYX and the C-terminal cysteine is CCYX.
>>
>> However, when I used pdb2gmx -ff amber99sb to get a .gro file, I 
>> receive several Long Bond warnings. I am working with a minimized 
>> structure, so I'm a bit confused as to why this is happening. Has 
>> anyone come up against this problem before?
> Have you checked the structure in Pymol or something like that?
>
>>
>> Many thanks,
>>
>> Max
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