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

[N-J.M. Macaluso]

Hi,

Yes, I've checked the original structure in both Pymol and Sybyl before 
performing pdb2gmx. However, after I received the error message about the 
bond lengths being to long, I took the .gro file generated by pdb2gmx, 
turned it back into a .pdb file using editconf, and the resulting structure 
looks like the molecule has exploded. The bond lengths are too long and the 
system is clearly corrupt, as the error states. So basically I start out 
with a reasonable structure, and then the pdb2gmx program with the 
Amber99sb force field generates an incorrect structure.

All of the atoms in the peptide are involved in the long bond warning. 
However, I am fairly certain the trouble rests in naming the terminal 
cysteine residues. Is there a problem with Amber naming of N- and C- 
terminal cysteins linked by a disulfide bond?

Thank you for your help,

Max

On May 26 2008, Yang Ye wrote:

>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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>>
>
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