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
/\
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|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
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Received on Mon Jul 06 2009 - 17:42:58 PDT
