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" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: [email protected]
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" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: "Discussion list for GROMACS users" <[email protected]>
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
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