[gmx-users] Problem with encad in pdb2gmx, GMX 3.3 CVS version

[David van der Spoel]

On Fri, 2005-10-28 at 00:01 -0300, Leonardo Sepulveda Durán wrote:
> Hello!!
> 
> I downloaded the last gromacs CVS version yesterday using 
> 
> 
> cvs -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs login
> cvs -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs co gmx
> cvs update -A -r release-3-3-patches 

Please do it like this instead:
cvs -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs login
cvs -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs co  -r \
release-3-3-patches gmx

Your original setup will give you a weird mix of 4.0beta and 3.3 code.

> 
> 
> I installed it as stated in the website. Then i  ran
> 
>  pdb2gmx -f 1YPC_met59.pdb -water f3c

As for the example below, please check the spacing in your pdb file.
Also you may have to subtract the first residue number in the error
message below.


> 
> This is part of the output
> 
> Making bonds...
> Opening library
> file /home/gromacs/LEONARDO/PROGRAMAS/bin/gmx/share/gromacs/top/aminoacids.dat
> Number of bonds was 1059, now 1059
> Generating angles, dihedrals and pairs...
> Before cleaning: 2808 pairs
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3
> Source code file: pgutil.c, line: 87
> 
> Fatal error:
> Atom CB not found in residue 64 while adding improper
> 
> -------------------------------------------------------
> 
> this are the first and last lines of the pdb i used
> 
> ATOM      1  N   MET I  20     -11.630   5.328   1.023  0.50 25.84
> ATOM      2  CA  MET I  20     -10.830   6.245   1.842  0.50 25.77
> ATOM      3  C   MET I  20     -10.600   7.583   1.122  1.00 25.46
> ATOM      4  O   MET I  20      -9.908   7.695   0.096  1.00 25.91
> ATOM      5  CB  MET I  20      -9.516   5.597   2.269  0.50 26.26
> ATOM      6  CG  MET I  20      -8.596   6.493   3.054  0.50 26.61
> ATOM      7  SD  MET I  20      -7.353   5.480   3.921  0.50 27.29
> ATOM      8  CE  MET I  20      -5.854   6.438   3.687  0.50 26.26
> ATOM      9  N   LYS I  21     -11.225   8.577   1.736  1.00 24.80
> (...)
> ATOM    497  O   VAL I  82      -1.544  11.982   3.001  1.00  8.33
> ATOM    498  CB  VAL I  82      -4.034  10.892   4.520  1.00  8.78
> ATOM    499  CG1 VAL I  82      -3.354   9.761   5.292  1.00  8.61
> ATOM    500  CG2 VAL I  82      -5.509  11.010   4.891  1.00  9.72
> ATOM    501  N   GLY I  83      -0.912  11.916   5.215  1.00  8.31
> ATOM    502  CA  GLY I  83       0.505  11.680   4.861  1.00  8.56
> ATOM    503  C   GLY I  83       1.524  12.137   5.881  1.00  8.72
> ATOM    504  O   GLY I  83       1.121  13.002   6.681  1.00  8.53
> ATOM    505  OXT GLY I  83       2.661  11.622   5.866  1.00  9.59
> TER     506      GLY I  83
> 
> 
> I am not sure if this is a bug; the residue 64(83) is a glycine, so I
> dont understand why it complains about CB atoms. When using opls
> pdb2gmx doesn't complain at all.
> 
> leonardo
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++