Hello Bill
Yes, I have unintentionally tried this before when including numerous peptides and not issuing the bond command for each separate peptide. Turns out that it worked fairly well for a single peptide, not so much when including multiple peptides and it pretty much resulted in the “analysis” suggested. The bond was not present, though neither was the CONECT info in the packmol output or the warning in leap.
I was curious if it was possible to confirm a correct disulphide bond using parmed/cpptraj or some other tool available in the prmtop/inpcrd file before initiating the simulations. Checking in VMD or Chimera was my first instinct though turns out that GUI software can sometimes render sulphide bonds if the distance criteria seems reasonable, even if these are not present for the simulation engine.
Best regards
// Gustaf
> On 14 Dec 2020, at 13:52, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> If you run MD in vacuum at 100K or more, it should become apparent if
> the bond is there.
>
> Bill
>
> On 12/14/20 12:54 AM, Gustaf Olsson wrote:
>> Hello everyone
>>
>> I just want to double check something.
>>
>> I ran packmol including a peptide with a disulphide bond, using only the one peptide packmol seems to have added the correct conect record in the produced PDB file:
>>
>> CONECT 9 52
>>
>> Then when I run leap with 'bond sys.2.SG go.7.SG’ and try to write top/crd files leap exits with an error:
>>
>> !FATAL: Message: 1-4: cannot add bond 14 95
>> This may be caused by duplicate bond specifications;
>> for example, explicit bond commands in addition to PDB conect records.
>>
>> Is it safe to assume that the correct conect record in my PDB file is correctly applied in leap or is this something which should be “stripped” from the PDB and the bond created using leap.
>>
>> Best regards
>> // Gustaf
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Received on Mon Dec 14 2020 - 05:30:03 PST
