[gmx-users] Neutral arginine; Charmm

[Sahil Lall]

Hi, 

I am trying to use neutral arginine for my work. Since the well
documented issues of nearly equivalent tautomeric protonated states, it
has not been implemented in the charmm forcefield. So, as suggested by
the charmm developers, I used methyl-guanidinium and Arginine as a
starting point and created a new neutral molecule [ ARN ] and made all
the appropriate changes wherever required. However, pdb2gmx is not
working as expected. 

Issue 1: No double bond seen between NE and CZ 

Issue 2: HH12 missing with error Warning: Long Bond (66-68 = 4.12787 nm)


the following are the residue parameters borrowed from MGU1 and ported
to make neutral arginine. 

[ ARN ]
[ atoms ]
N NH1 -0.470 0
HN H 0.310 1
CA CT1 0.070 2
HA HB1 0.090 3
CB CT2 -0.180 4
HB1 HA2 0.090 5
HB2 HA2 0.090 6
CG CT2 -0.180 7
HG1 HA2 0.090 8
HG2 HA2 0.090 9
CD CT2 0.060 10
HD1 HA2 0.090 11
HD2 HA2 0.090 12
NE NG2D1 -0.860 13
CZ CG2N1 0.660 14
NH1 NG321 -0.600 15
HH11 HGPAM2 0.290 16
HH12 HGPAM2 0.290 17
NH2 NG321 -0.600 18
HH21 HGPAM2 0.290 19
HH22 HGPAM2 0.290 20
C C 0.510 21
O O -0.510 22
[ bonds ]
CB CA
CG CB
CD CG
NE CD
CZ NE
NH2 CZ
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CG HG1
CG HG2
CD HD1
CD HD2
CZ NH1
NH1 HH11
NH1 HH12
NH2 HH21
NH2 HH22
O C
[ impropers ]
N -C CA HN
C CA +N O
CZ NE NH1 NH2
NH1 HH11 HH12 CZ
NH2 HH21 HH22 CZ
[ cmap ]
-C N CA C +N 

-- 

Sahil