Hi Dr.Case,
I have tried to edit leaprc.ff14SB as per your suggestion
1. modify (a local copy of) the leaprc.protein.ff14SB file, removing the
addPdbResMap block. This will tell leap that the beginning and ending
residues are to be "non-terminal" residues (since that is what they will be
after the cyclization).
But stil it is not giving me cyclic structure.
Thanking you,
Abhishek
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Thursday, October 20, 2016 5:35:44 AM
To: AMBER Mailing List
Subject: Re: [AMBER] frcmod file error
On Thu, Oct 20, 2016, Thakur, Abhishek wrote:
>
> Thank you for your suggestion, I think I have a cyclic peptide of around
> 75 atoms, so I think that is why antechamber is not working.
To make a cyclic peptide, you have to three things (generally):
1. modify (a local copy of) the leaprc.protein.ff14SB file, removing the
addPdbResMap block. This will tell leap that the beginning and ending
residues are to be "non-terminal" residues (since that is what they will be
after the cyclization).
2. add the "bond" command to the tleap input to create a bond between the C of
the last residue and the N of the first residue.
3. generate a reasonable starting structure for the cyclized peptide.
Step 3 has been discussed earlier. I think you missing Step 1, and hence
trying to make a bond between atom types C and N3, rather than C and N.
...hope this helps...dac
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Received on Thu Oct 20 2016 - 11:30:02 PDT
