[AMBER] Generating the parameters of a peptide sequence consisting of non-standard amino-acid

From: RITUPARNA ROY <ritup176122023.iitg.ac.in>
Date: Thu, 10 Oct 2019 15:37:12 +0000

Dear all,

I am trying to generate the prmtop and inpcrd files for the peptide sequence NFXAXL, where X is 2-amino benzoic acid.

Using the mol2 file of the optimized structure of 2-amino benzoic acid, I generated the prepi and frcmod files using antechamber, following the tutorial, http://ambermd.org/tutorials/basic/tutorial5/index.htm

antechamber -fi mol2 -i ortho.mol2 -bk OAB -fo ac -o ortho.ac -c bcc -at amber
prepgen -i ortho.ac -o ortho.prepi -f prepi -m mainchain.ortho -rn OAB -rf ortho.res
parmchk2 -i ortho.prepi -f prepi -o ortho-gaff.frcmod -a Y -p /home/ritu/softwares/Amber/amber18/dat/leap/parm/parm10.dat
parmchk2 -i ortho.prepi -f prepi -o ortho-14sb.frcmod

Then I used tleap to add 2-amino benzoic acid residue to a peptide sequence of standard amino-acid residues.

source leaprc.protein.ff14SB
loadamberprep ortho.prepi
loadamberparams ortho-gaff.frcmod
loadamberparams ortho-14sb.frcmod
m = sequence {NASN PHE GLY ALA OAB CLEU}
savepdb m ortho-pep.pdb
saveamberparm m ortho-pep.prmtop ortho-pep.inpcrd

Generating the parameter files gives the following error:

/home/ritu/softwares/Amber/amber18/bin/teLeap: Error!
 ** No torsion terms for CX-C-N2-CA

/home/ritu/softwares/Amber/amber18/bin/teLeap: Error!
 ** No torsion terms for HA-CA-N-H

/home/ritu/softwares/Amber/amber18/bin/teLeap: Error!
 ** No torsion terms for HA-CA-N-CX

/home/ritu/softwares/Amber/amber18/bin/teLeap: Error!
 ** No torsion terms for CA-CA-N-H

/home/ritu/softwares/Amber/amber18/bin/teLeap: Error!
 ** No torsion terms for CA-CA-N-CX

/home/ritu/softwares/Amber/amber18/bin/teLeap: Error!
 ** No torsion terms for CA-CA-N-H

/home/ritu/softwares/Amber/amber18/bin/teLeap: Error!
 ** No torsion terms for CA-CA-N-CX
Building improper torsion parameters.
old PREP-specified impropers:
 <OAB 5>: -M C3 N11 H12
 <OAB 5>: C4 C2 C3 N11
 <OAB 5>: C3 C1 C2 H8
 <OAB 5>: C2 C6 C1 H7
 <OAB 5>: C5 C1 C6 H10
 <OAB 5>: C14 C5 C4 C3
 <OAB 5>: C4 +M C14 O15
 <OAB 5>: C4 C6 C5 H9
 total 23 improper torsions applied
 8 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.

/home/ritu/softwares/Amber/amber18/bin/teLeap: Warning!
Parameter file was not saved.

I had tried this exact same method to generate the parameters of the NF(Me-G)A(Me-I)L, where both the G and I residues were N-methylated and it gave the desired results.
Kindly help to generate the parameters of the peptide sequence.

Rituparna Roy,

Junior Research Fellow,

Department of Chemistry,

Indian Institute of Technology Guwahati.
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Received on Thu Oct 10 2019 - 09:00:02 PDT
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