[AMBER-Developers] Problems with leaprc.ff99SB and DNA

From: Ross Walker <ross.rosswalker.co.uk>
Date: Mon, 6 Jul 2009 22:57:26 +0100

Hi All,

I noticed recently that the latest updates to the leaprc.ff99SB:

revision 10.2
date: 2009/06/17 11:55:47; author: case; state: Exp; lines: +0 -1
remove the CG atom hybridization defintion: never used, and conflicts with
GLYCAM
----------------------------
revision 10.1
date: 2009/04/28 14:19:39; author: case; state: Exp; lines: +19 -13
update to pdb format 3: allows correct identification of RNA vs DNA
----------------------------

Breaks the Tutorial B1 on the AMBER website. The major change is:

AMBER10
  { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" }
  { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" }
  { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" }
  { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" }
  { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" }
  { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" }
  { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" }
  { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" }
  { 0 "C5" "DC5" }
  { 0 "G5" "DG5" }
  { 0 "A5" "DA5" }
  { 0 "T5" "DT5" }
  { 1 "C3" "DC3" }
  { 1 "G3" "DG3" }
  { 1 "A3" "DA3" }
  { 1 "T3" "DT3" }


AMBER11 CVS
  { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" }
  { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" }
  { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" }
  { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" }
  { 0 "G" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" }
  { 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" }
  { 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" }
  { 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" }
  { 0 "DG" "DG5" } { 1 "DG" "DG3" }
  { 0 "DA" "DA5" } { 1 "DA" "DA3" }
  { 0 "DC" "DC5" } { 1 "DC" "DC3" }
  { 0 "DT" "DT5" } { 1 "DT" "DT3" }

This results in the second chain in the file nuc_ter.pdb (attached) not
being recognized. This is produced with nucgen and then the TER card is
manually added between the chains.

...
ATOM 21 N1 A5 1 0.658 -0.554 -0.030
ATOM 22 P A 2 4.562 -7.653 1.300
...
ATOM 205 N1 A 9 -0.324 -0.797 27.010
ATOM 206 P A3 10 -5.869 -6.704 28.340
...
ATOM 248 C7 T5 11 0.583 5.368 31.000
ATOM 249 P T 12 8.189 3.510 29.120
...
ATOM 416 C7 T 19 -4.925 2.214 3.960
ATOM 417 P T3 20 -0.808 8.873 2.080

So looking at the changes above I think the A5's, A3's, T5's, T3's and T's
are no longer recognized while the A is miss recognized as RNA. Should we
re-update leaprc.ff99SB? Or update nucgen to use the new residue names?

All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.





Received on Mon Jul 06 2009 - 17:42:58 PDT
Custom Search