[gmx-users] tfe

[Justin A. Lemkul]

shahrbanoo karbalaee wrote:

> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> ; Include water topology
> #include "spce.itp"
> Include tfe topology
> #include "tfe.itp"
> 
> #endif
> 

Well, there's the problem.  You've enclosed the SPC/E and TFE .itp files within 
an #ifdef/#endif block, so they only get included with -DPOSRES.  Move spce.itp 
and tfe.itp from within this block and things should work fine.

-Justin

> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> 
> #endif
> 
> ; Include generic topology for ions
> #include "ions.itp"
> 
> [ system ]
> ; Name
> PEPTIDE A5 OR AUREIN 1.2 in 30%tfe  water
> 
> [ molecules ]
> ; Compound        #mols
> Protein_A           1
> SOL               941
> tfe               301
> 
> ---------------------------------------------------
>  and the file tfe.gro is:
> 
> Glycine aRginine prOline Methionine Alanine Cystine Serine
>     9
>     1TFE    CC'    1  -0.098  -0.156   0.352
>     1TFE    FD'    2  -0.010  -0.129   0.451
>     1TFE    FE'    3  -0.143  -0.282   0.370
>     1TFE    FF'    4  -0.203  -0.072   0.366
>     1TFE    CB'    5  -0.033  -0.140   0.217
>     1TFE   HB'1    6  -0.106  -0.161   0.139
>     1TFE   HB'2    7   0.051  -0.209   0.209
>     1TFE    O2'    8   0.014  -0.006   0.204
>     1TFE    HO2    9   0.055   0.005   0.118
>    0.00000   0.00000   0.00000
> 
> 
> thanks and best regards

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

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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