Hi Dr.Case,
I was unable to find any file name leaprc.protein.ff14SB
I have found leaprc.ff14SB under /amber14/dat/leap/cmd
More over there is addPdbResMap {
Should I delete the parenthesis also?
________________________________
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DQICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=SLGixl-cb3XmsMcdRehrgzinDOVKYacIKryMQ_DFUo4&s=ncqn6E6SjNbH_w0LLyTb98lN1phpp1wHQS1Ang8xCX4&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 20 2016 - 10:00:05 PDT
