[gmx-users] Neutral arginine; Charmm

[Justin Lemkul]

On 12/10/19 4:26 AM, Sahil Lall wrote:
> 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

This isn't an actual problem. Visualization software will render things 
differently but these visualizations have no bearing on the topology.

As long as the CD-NE-CZ angle is set correctly, you should get the 
proper geometry.

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

A missing H atom should not trigger a long bond warning; this usually 
indicates a problem in the backbone but in any case means you have bad 
coordinates. Look at atoms 66 and 68.

If you're missing an H that means you need to either rename the atoms in 
the input coordinate file or write a suitable .hdb entry to have them 
generated.

-Justin

>
> 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
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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