[AMBER] To get resp charges of a modified central residue (not an integer).

From: Baptiste Legrand <bap.legrand.gmail.com>
Date: Tue, 15 Jul 2014 17:24:52 +0200

Dear all,

I tried diverses strategies to get resp charges of an exotic amino acid
(a dipeptide actually) and to incorporate it in a peptide sequence but
without success (not an integer) . Can you give me your opinion, please?
For example:

First, I built a pdb of my modified residue (NH2-MOD-COOH) then I
launched antechamber:
antechamber -i MOD.pdb -fi pdb -o ./MOD.prepin -fo prepi -c bcc -s 2 >
parmchk -i MOD.prepin -f prepi -o MOD.frcmod (and I completed the frcmod
file manually to fit parm99.dat)

In parallel, I built the ACE-MOD-NME fragment (MOD-cap.pdb) to derive
the charge using the RED server and to modify the charges directly in
the prepin.

Then, I used leap:

source leaprc.gaff
source leaprc.ff99SB
loadamberprep MOD.prepin
loadamberparams MOD.frcmod
remove MOD MOD.1.H29 (remove a H from the NH2)
remove MOD MOD.1.H30 (remove the H from the COOH)
set MOD head MOD.1.N1
set MOD tail MOD.1.C5
tri = sequence { NALA MOD CALA}
saveamberparm tri tri.prmtop tri.inpcrd

Finally, except the charges, the generated files seems to be correct. I
also tried to calculate the charges only using antechamber and/or via a
mol2 file generating a new library.

Best wishes.


AMBER mailing list
Received on Tue Jul 15 2014 - 08:30:02 PDT
Custom Search