I created the waterbox using the following tutorial:
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node7.html
In t-leap, first i generate a new pdb because i need to rename the
number of residues because i have the different monomers, so in this
way, i obtain one.
After, i load this pdb and follow the next steps:
Welcome to LEaP!
Sourcing leaprc: /opt/amber10//dat/leap/cmd/leaprc
Log file: ./leap.log
Loading parameters: /opt/amber10//dat/leap/parm/parm94.dat
Loading library: /opt/amber10//dat/leap/lib/all_nucleic94.lib
Loading library: /opt/amber10//dat/leap/lib/all_amino94.lib
Loading library: /opt/amber10//dat/leap/lib/all_aminoct94.lib
Loading library: /opt/amber10//dat/leap/lib/all_aminont94.lib
Loading library: /opt/amber10//dat/leap/lib/ions94.lib
Loading library: /opt/amber10//dat/leap/lib/water.lib
loadAmberParams parm99.dat
loadpdb xxxx.pdb (this is the pdb with the new atom numeration)
the result i obtain is :
.......
(Residue 9990: WAT, Terminal/last, was not found in name map.)
(Residue 9991: WAT, Terminal/last, was not found in name map.)
(Residue 9992: WAT, Terminal/last, was not found in name map.)
(Residue 9993: WAT, Terminal/last, was not found in name map.)
(Residue 9994: WAT, Terminal/last, was not found in name map.)
(Residue 9995: WAT, Terminal/last, was not found in name map.)
(Residue 9996: WAT, Terminal/last, was not found in name map.)
(Residue 9997: WAT, Terminal/last, was not found in name map.)
(Residue 9998: WAT, Terminal/last, was not found in name map.)
(Residue 9999: , Terminal/last, was not found in name map.)
Unknown residue: number: 9999 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Joining NGLU - ALA
Joining ALA - SER
Joining SER - SER
Joining SER - ALA
Joining ALA - PHE
Joining PHE - ILE
Joining ILE - VAL
Joining VAL - VAL
.....
Creating new UNIT for residue: sequence: 10000
Created a new atom named: within residue: .R< 10000>
total atoms in file: 191739
The file contained 1 atoms not in residue templates
Fer
El mié, 17-02-2010 a las 12:45 -0500, case escribió:
> On Wed, Feb 17, 2010, Fernando Martín García wrote:
> >
> > I've generated a waterbox using VMD. The total number of atoms of my
> > system is more than 190000.
> >
> > When i try to generate the topology and coordinate files with tleap, it
> > only recognizes until 9999 residue, so the box is incomplete.
>
> Can you show what commands you used, and what the actual error message is?
>
> ...thanks...dac
>
>
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--
Fernando Martín García.
Centro de Biología Molecular "Severo Ochoa".
C/ Nicolás Cabrera, 1.
Campus UAM. Cantoblanco, 28049 Madrid. Spain.
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Received on Thu Feb 18 2010 - 00:00:03 PST
