3
$\begingroup$

I am looking for CHARMM36 parameters for Neutral Arginine. Protonated form of Argnine is already available in CHARMM36 library, but not the same for Neutral. Thanks.

With best regards

$\endgroup$

1 Answer 1

3
$\begingroup$

A quick search of the toppar folder in CHARMM shows that there are three patches that are available to create neutral arginine from the charged arginine.

This is the sample input

* Reads the DCA residue from the stream topology file and writes a pdb consisting
* of a single DCA molecule
*

bomlev -5
wrnlev -5

!topology and parameter files
open read card unit 10 name ./toppar/top_all36_prot.rtf
read  rtf card unit 10 

open read card unit 20 name ./toppar/par_all36m_prot.prm
read para card unit 20 flex

stream ./toppar/toppar_all36_prot_arg0.str

read sequence ARG 1
generate ARG first nter last cter

ic generate
ic param
ic seed 1 N 1 CA 1 C 
ic build
print ic

coor build
coor print
hbuild sele all end

mini sd 10000 1000

open write card unit 30 name arginine_charged.pdb
write coor pdb  unit 30
close unit 30

patch RN1 ARG 1
autogen angle dihe 
ic build
coor build

open write card unit 30 name arginine_neutral.pdb
write coor pdb  unit 30

close unit 30
$\endgroup$

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .