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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