[gmx-users] encad problems

[Alexander Benedix]

hi,
i wanted to test encad and experienced some problems (i have some 
solutions, but i do not know, whether they are right or wrong)...
in the case of the scaled down vacuum charges my ASP has a total charge 
of -0.2 as you can see from my topology:

    16         N1      2    ASP      N      7     -0.333    14.0067   ; 
qtot -0.333
    17         HN      2    ASP      H      7      0.333      1.008   ; 
qtot 0
    18         C1      2    ASP     CA      8     -0.119     12.011   ; 
qtot -0.119
    19          H      2    ASP     HA      8      0.119      1.008   ; 
qtot 0
    20         C2      2    ASP     CB      9     -0.238     12.011   ; 
qtot -0.238
    21          H      2    ASP    HB1      9      0.119      1.008   ; 
qtot -0.119
    22          H      2    ASP    HB2      9      0.119      1.008   ; 
qtot 0
    23       Abis      2    ASP     CG     10       0.64     12.011   ; 
qtot 0.64
    24       Obis      2    ASP    OD1     10      -0.42    15.9994   ; 
qtot 0.22
    25       Obis      2    ASP    OD2     10      -0.42    15.9994   ; 
qtot -0.2
    26     Aprime      2    ASP      C     11       0.38     12.011   ; 
qtot 0.18
    27          O      2    ASP      O     11      -0.38    15.9994   ; 
qtot -0.2

maybe it's a typo in ffencadv.rtp for OD1/OD2 and it should be -0.32? i 
did not checked yet, but according to the topology the same problem 
should occur with GLU. i doubt that the protein should be partially 
charged in total.
and in ffencadv-c.tbd i had to change (same for ffencads-c.tbd)

[ COOH ]
...
[ impropers ]
O2    CA    C    O1    improper_X_X_A_X

to

[ COOH ]
...
[ impropers ]
OT    CA    C    O    improper_X_X_A_X

in order to get it working (with neutral cooh-terminals).
i am not sure if i am right.

regards,
alexander



-- 
***********************************************************************
Dipl.-Phys. Alexander Benedix
Zentrum für Bioinformatik Saar
Theoretical & Computational Membrane Biology
Universität des Saarlandes
Building C7.1,    Room 0.07,    Phone x-64179
eMail:  benedix at bioinf.uni-sb.de
aim:    wizkah
icq:    268065902
Url:    http://www.bioinf.uni-sb.de/RB/