Please send me directly your pdb and rtp file. I will see how to resolve
this issue.
Regards,
Yang Ye
On 1/4/2007 7:23 AM, yuemin liu wrote:
This is a good idea. But here comes following major
complaints: "Atom H4 not found in rtp database in
residue ASO, it looks a bit like H1". Does the group
number matters? I assigned the bulky side chain as one
group number 4. Should the H4 comes with O4? I check
my rtp file, O4 is connected to C4 and CBO. Atom type
of O4 is OS which is sugar or ester oxygen, therefore
no need H4 at all. So, what is likely the reason the
program kept asking for H*? For better reference,
large portion of the output is also give below.
Thanks a lot,
Yuemin Liu
Opening library file ffgmx.rtp
Opening library file aminoacids.dat
Reading asomh9smgm3.pdb...
Read 139 atoms
Opening library file xlateat.dat
26 out of 26 lines of xlateat.dat converted
succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1
residues with 139 atoms
chain #res #atoms
1 ' ' 1 139
All occupancy fields zero. This is probably not an
X-Ray structure
Opening library file ffgmx.atp
Atomtype 54
Reading residue database... (ffgmx)
Opening library file ffgmx.rtp
Residue 99
Sorting it all out...
Opening library file ffgmx.hdb
Opening library file
/usr/share/gromacs/top/ffgmx-n.tdb
Opening library file
/usr/share/gromacs/top/ffgmx-c.tdb
Back Off! I just backed up min-model.top to
./#min-model.top.2#
Processing chain 1 (139 atoms, 1 residues)
There are 2 donors and 2 acceptors
There are 2 hydrogen bonds
Checking for duplicate atoms....
Opening library file specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
N-terminus: NH3+
C-terminus: COO-
Now there are 1 residues with 277 atoms
Making bonds...
Opening library file aminoacids.dat
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3
Source code file: add_par.c, line: 221
Fatal error:
Atom H4 not found in rtp database in residue ASO, it
looks a bit like H1
--- Yang Ye <[EMAIL PROTECTED]> wrote:
To debug this problem. I suggest you to create a pdb
file which contains
only ASO residue and play with pdb2gmx.
Regards,
Yang Ye
On 1/4/2007 1:26 AM, yuemin liu wrote:
It does not work either. Thanks anyway. I doubt
the
error results from sth else. Most likely the
reason is
default angle and dihedral values in the modified
ffgmxbon.itp file. By the way, how would you
assign
default angle and dihedral values? Structurally it
is
fine unless the size matters, because the new
amino
acid has almost 200 atoms.
Best wishes,
--- Yang Ye <[EMAIL PROTECTED]> wrote:
Hi,
You may try Dr Mu's suggestion:
check file xlateat.dat and find any line matching
protein XXX H1
XXX could be any name of an atom. Remove this
line
and decrement the
number on the top.
Regards,
Yang Ye
On 1/3/2007 11:18 PM, yuemin liu wrote:
I did add the resname in aminoacids.dat and also
change the the number on the top. It still
complains
same thing. It is H atom type also name H
(connecting
to N) in the new amino acid like the regular
amino
acid, and has nothing to do with H1 at all.
Thanks,
Liu, Yuemin
--- Yang Ye <[EMAIL PROTECTED]> wrote:
You may try add residue name ASO to the end of
/top/aminoacids.dat and
also increment the number on the top.
Regards,
Yang Ye
On 1/3/2007 8:55 AM, yuemin liu wrote:
Hi, Everyone,
I got Error when adding a unnatural amio acid
in
a
protein. I have all the rtp and hdb file
modified
using information either from ffgmx.rtp
ffgmx.hdb
or
thr rtp file form progdrg. There is no H1 in
either
rtp file or my new pdb file. When I try use
pdb2gmx to
generate top file, it always give the error
message
following;
"Atom H1 not found in rtp database in residue
ASO,
it
looks a bit like H". I know it refers to the
Hydrogen
of the peptide bond which has nothing wrong
there.
Hope can get help from you with this,
Thanks,
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