[gmx-users] Error in Energy Minimization

[Sunny]

Hi,

Continue to the energy minimization problem. I use l-bfgs to run the energy 
minimization for the structure summarized in the previous message below. The 
em output topology confout.gro doesn't contain velocity data. Then, I try to 
convert confout.gro into .pdb format by:

editconf -f confout.gro -o confout.pdb

The editconf command creates an empty confout.pdb file and gives the 
message:

Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file /usr/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Read 12918 atoms
Volume: 727.344 nm^3, corresponds to roughly 327300 electrons
No velocities found

Is the output of l-bfgs does contain velocities? How can I convert it to a 
.pdb file?

Thanks,

George

>From: "Sunny" <ge_sunny at hotmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Error in Energy Minimization
>Date: Tue, 16 Jan 2007 15:28:13 +0000
>
>Hi Tsjerk,
>
>The system has 1 protein (118 atoms) and 256 DPPC lipids (12800 atoms) 
>without solvent. The box size is 6.125, 12.5, 9.5 nm. The make_ndx output 
>is as follows. I can run l-bfgs on the structure.
>
>Analysing residue names:
>Opening library file 
>/usr/local/packages/gromacs/g_3.3.1/share/gromacs/top/aminoacids.dat
>There are:   256      OTHER residues
>There are:    12    PROTEIN residues
>There are:     0        DNA residues
>Analysing Protein...
>Analysing Other...
>
>  0 System              : 12918 atoms
>  1 Protein             :   118 atoms
>  2 Protein-H           :    89 atoms
>  3 C-alpha             :    12 atoms
>  4 Backbone            :    36 atoms
>  5 MainChain           :    49 atoms
>  6 MainChain+Cb        :    58 atoms
>  7 MainChain+H         :    63 atoms
>  8 SideChain           :    55 atoms
>  9 SideChain-H         :    40 atoms
>10 Prot-Masses         :   118 atoms
>11 Non-Protein         : 12800 atoms
>12 DPP                 : 12800 atoms
>13 Other               : 12800 atoms
>
>George
>
>>From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
>>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>>Subject: Re: [gmx-users] Error in Energy Minimization
>>Date: Tue, 16 Jan 2007 13:31:15 +0100
>>
>>Hi George,
>>
>>You didn't mention whether this was with or without solvent. This is
>>probably due to an error in your starting structure, and I advice to
>>check it carefully. Also, if you're running in solvent, check your
>>box.
>>
>>>Step=   57, Dmax= 4.3e-03 nm, Epot= -1.79963e+23 Fmax=         inf, atom= 
>>>2
>>
>>The only thing I don't really get is this potential energy. Can you
>>give more details about your system? Type of molecules, size, etc?
>>
>>Cheers,
>>
>>Tsjerk
>>
>>--
>>Tsjerk A. Wassenaar, Ph.D.
>>Junior UD (post-doc)
>>Biomolecular NMR, Bijvoet Center
>>Utrecht University
>>Padualaan 8
>>3584 CH Utrecht
>>The Netherlands
>>P: +31-30-2539931
>>F: +31-30-2537623
>>_______________________________________________
>>gmx-users mailing list    gmx-users at gromacs.org
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>
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