>>>It's not clear how you generated the new pdb...
I generated it loading the pdb that comes from VMD, in the tleap and
saving using:
savepdb unit xxx.pdb
>>>What does your pdb file look like around residue 9999?
ATOM 36679 H1 WAT 9998 58.470 233.602 -63.146 1.00 0.00
ATOM 36680 H2 WAT 9998 59.839 233.882 -63.685 1.00 0.00
ATOM 36681 O WAT 9998 59.235 233.159 -63.543 1.00 0.00
TER
ATOM 36682 H1 WAT 9999 100.660 225.751 -55.788 1.00 0.00
ATOM 36683 H2 WAT 9999 101.715 225.119 -56.819 1.00 0.00
ATOM 36684 O WAT 9999 100.965 224.888 -56.242 1.00 0.00
TER
ATOM 36685 H1 WAT 10000 110.499 217.338 -64.183 1.00 0.00
ATOM 36686 H2 WAT 10000 109.973 216.163 -63.407 1.00 0.00
ATOM 36687 O WAT 10000 109.886 217.133 -63.489 1.00 0.00
TER
ATOM 36688 H1 WAT 10001 64.049 225.777 -59.095 1.00 0.00
ATOM 36689 H2 WAT 10001 65.473 226.391 -58.951 1.00 0.00
ATOM 36690 O WAT 10001 64.598 226.525 -59.360 1.00 0.00
TER
ATOM 36691 H1 WAT 10002 111.563 208.213 -64.646 1.00 0.00
ATOM 36692 H2 WAT 10002 111.591 206.890 -65.390 1.00 0.00
ATOM 36693 O WAT 10002 111.439 207.274 -64.502 1.00 0.00
The problem is the next. I have tried to build a rectangular box for my
proteins, so my protein will be in one of the side of the box. To do
that i followed the tutorial of VMD. I obtained a pdb with the protein
and water. I use tleap to rename the number of the residues of the three
monomers:
x = loadpdb vmd_output.pdb
savepdb x tleap_output.pdb
The next step is to load again this new structure (tleap_output.pdb),
but here i have the problem i explained:
(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
The solution that i found is the next. I load a protein (without water)
and with 8 water (with different name but same atom type) in the
coordinates of the corners of my box:
ap parm99.dat
x = loadpdb xxx.pdb
solvatebox x WATBOX216 1 (only 1 ansgtrom and then the size of my box
doesn't change a lot)
addions x Na+ 15
sap x topology.tpp coordinate.tpp
In this way a don't have any problem to generate my pdb and work with
dynamics.
Fer
El jue, 18-02-2010 a las 07:37 -0500, David A. Case escribió:
> On Thu, Feb 18, 2010, Fernando Martín García wrote:
>
> > In t-leap, first i generate a new pdb
>
> It's not clear how you generated the new pdb...
>
> > (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
>
> What does your pdb file look like around residue 9999?
> > Creating new UNIT for residue: sequence: 10000
> > Created a new atom named: within residue: .R< 10000>
>
> ....dac
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
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 - 06:00:02 PST
