[gmx-users] problem with pdb2gmx to generate top file

[Justin A. Lemkul]

Moeed wrote:
> Hello,
> 
> I am trying to generate gro and top file with pdb2gmx program. I have 
> made a copy of ffoplsaa.rtp from library to working directory and added 
> Hexane molecule residue to the beginning of the ffoplsaa.rtp.

<snip>

>I type in:
> 
> 
> pdb2gmx -f Hexane-PRODRG.pdb -o Hexane-PRODRG.gro -p Hexane-PRODRG.top 
> -ff oplsaa >& output.pdb2gmx
> 

In principal, this should work, but if it's not, then stop redirecting your 
output (i.e., let it print to the screen) and see what pdb2gmx is doing. 
Otherwise, inspect this "output.pdb2gmx" for error messages, etc.

-Justin

> I do not get gro file at all and top file I get contains the following 
> comments only!:
> 
> ;********************************************************************
> ;       File 'Hexane-PRODRG.top' was generated
> ;       By user: moeed (500)
> ;       On host: moeed-desktop
> ;       At date: Sun May  9 10:47:26 2010
> ;
> ;       This is your topology file
> ;       "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra)
> ;
> ; Include forcefield parameters
> #include "ffoplsaa.itp"
> 
> 
> 
> ***************************************
> 
> 
> 
> 
> 
> 
> ***************Hexane-PRODRG.pdb
> 
> CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1           1
> ATOM      1  C1      HEX 1       8.330   1.510  -0.010  0.00  
> 0.00           C
> ATOM      2  H11     HEX 1       9.281   1.200  -0.024  0.00  
> 0.00           H
> ATOM      3  H12     HEX 1       8.154   2.080  -0.813  0.00  
> 0.00           H
> ATOM      4  H13     HEX 1       8.166   2.044   0.820  0.00  
> 0.00           H
> ATOM      5  C2      HEX 1       7.400   0.300  -0.030  0.00  
> 0.00           C
> ATOM      6  H21     HEX 1       7.584  -0.267   0.773  0.00  
> 0.00           H
> ATOM      7  H22     HEX 1       7.573  -0.231  -0.860  0.00  
> 0.00           H
> ATOM      8  C3      HEX 1       5.940   0.730  -0.010  0.00  
> 0.00           C
> ATOM      9  H31     HEX 1       5.754   1.291  -0.816  0.00  
> 0.00           H
> ATOM     10  H32     HEX 1       5.769   1.266   0.817  0.00  
> 0.00           H
> ATOM     11  C4      HEX 1       5.010  -0.480  -0.020  0.00  
> 0.00           C
> ATOM     12  H41     HEX 1       5.192  -1.038   0.790  0.00  
> 0.00           H
> ATOM     13  H42     HEX 1       5.186  -1.020  -0.843  0.00  
> 0.00           H
> ATOM     14  C5      HEX 1       3.540  -0.050  -0.010  0.00  
> 0.00           C
> ATOM     15  H51     HEX 1       3.357   0.507  -0.820  0.00  
> 0.00           H
> ATOM     16  H52     HEX 1       3.363   0.489   0.813  0.00  
> 0.00           H
> ATOM     17  C6      HEX 1       2.610  -1.270  -0.020  0.00  
> 0.00           C
> ATOM     18  H61     HEX 1       1.658  -0.964  -0.013  0.00  
> 0.00           H
> ATOM     19  H62     HEX 1       2.780  -1.812  -0.843  0.00  
> 0.00           H
> ATOM     20  H63     HEX 1       2.785  -1.830   0.790  0.00  
> 0.00           H
> END
> ************************************************************************************************
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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