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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Phobrain.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 14 2020 - 05:00:03 PST
