[gmx-users] new CHARMM-GUI output not supported?

[Albert]

Hello:


  I obtained a  POPC lipids from CHARMM-GUI and I found the initial 12 
line are following:
following atom name order:

ATOM   6315  N   POPC   22       3.580 -22.614  19.970 1.00-19.29      MEMB
ATOM   6316  C12 POPC   22       4.563 -22.414  18.821 1.00-17.85      MEMB
ATOM   6317 H12A POPC   22       4.337 -21.455  18.379  1.00 0.00      MEMB
ATOM   6318 H12B POPC   22       5.583 -22.427  19.173  1.00 0.00      MEMB
ATOM   6319  C13 POPC   22       3.979 -23.730  20.844 1.00-17.96      MEMB
ATOM   6320 H13A POPC   22       3.969 -24.679  20.329  1.00 0.00      MEMB
ATOM   6321 H13B POPC   22       4.977 -23.582  21.229  1.00 0.00      MEMB
ATOM   6322 H13C POPC   22       3.420 -23.829  21.763  1.00 0.00      MEMB
ATOM   6323  C14 POPC   22       3.424 -21.320  20.778 1.00-20.44      MEMB
ATOM   6324 H14A POPC   22       2.552 -21.497  21.391  1.00 0.00      MEMB
ATOM   6325 H14B POPC   22       4.281 -21.118  21.404  1.00 0.00      MEMB
ATOM   6326 H14C POPC   22       3.249 -20.474  20.130  1.00 0.00      MEMB


And here is initial 12 line Slipid popc.itp:
; residue   1 POPC rtp POPC q  0.0
      1        NTL      1   POPC      N      1       -0.6 14.007 ; qtot 
-0.6
      2       CTL2      1   POPC    C12      2       -0.1 12.011 ; qtot 
-0.7
      3       CTL5      1   POPC    C13      3      -0.35 12.011 ; qtot 
-1.05
      4       CTL5      1   POPC    C14      4      -0.35 12.011 ; qtot 
-1.4
      5       CTL5      1   POPC    C15      5      -0.35 12.011 ; qtot 
-1.75
      6         HL      1   POPC   H12A      6       0.25 1.008   ; qtot 
-1.5
      7         HL      1   POPC   H12B      7       0.25 1.008   ; qtot 
-1.25
      8         HL      1   POPC   H13A      8       0.25 1.008   ; qtot -1
      9         HL      1   POPC   H13B      9       0.25 1.008   ; qtot 
-0.75
     10         HL      1   POPC   H13C     10       0.25 1.008   ; qtot 
-0.5
     11         HL      1   POPC   H14A     11       0.25 1.008   ; qtot 
-0.25
     12         HL      1   POPC   H14B     12       0.25 1.008   ; qtot 0


And here is initial 12 line in CHARMM36.ff/lipids.rtp file:

[ POPC ]
  [ atoms ]
     N    NTL    -0.60    0
     C12    CTL2    -0.10    1
     C13    CTL5    -0.35    2
     C14    CTL5    -0.35    3
     C15    CTL5    -0.35    4
     H12A    HL    0.25    5
     H12B    HL    0.25    6
     H13A    HL    0.25    7
     H13B    HL    0.25    8
     H13C    HL    0.25    9
     H14A    HL    0.25    10
     H14B    HL    0.25    11


As we can see the Slipids popc.itp is the same with CHARMM36.ff/lipids.rtp
, but both of which are different from current CHARMM-GUI output. 
Probably CHARMM-GUI
change its format, and Slipids FF and CHARMM36 FF in Gromacs cannot 
support current new version
CHARMM-GUI output?

Moreover, the new CHARMM36 FF (both for protein, lipids and 
ions)introduced  Residue pair specific (native contact) non-bonded 
parameters, nbfix term,
probably it is also not supported in current CHARMM36FF in Gromacs?

  thank you very much

best
Albert



-------------- next part --------------
An embedded message was scrubbed...
From: Shuguang Yuan <shuguang.yuan at epfl.ch>
Subject: new CHARMM-GUI output not supported?
Date: Tue, 16 Apr 2013 06:26:04 +0200
Size: 4343
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20130416/f1656522/attachment.eml>