[gmx-users] Error when adding a unnatural amio acid
yuemin liu
liucan1 at yahoo.com
Thu Jan 4 00:23:24 CET 2007
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 <leafyoung81-group at yahoo.com> 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 <leafyoung81-group at yahoo.com> 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 <leafyoung81-group at yahoo.com> 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,
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>
> __________________________________________________
> >>
> >>>>> Do You Yahoo!?
> >>>>> Tired of spam? Yahoo! Mail has the best spam
> >>>>>
> >>>>>
> >>>> protection around
> >>>>
> >>>>
> >>>>> http://mail.yahoo.com
> >>>>>
> _______________________________________________
> >>>>> gmx-users mailing list
> gmx-users at gromacs.org
> >>>>>
> >>>>>
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>
> >>>>> Please don't post (un)subscribe requests to
> the
> >>>>>
> >>>>>
> >>>> list. Use the
> >>>>
> >>>>
> >>>>> www interface or send it to
> >>>>>
> >>>>>
> >>>> gmx-users-request at gromacs.org.
> >>>>
> >>>>
> >>>>> Can't post? Read
> >>>>>
> >>>>>
> >>>> http://www.gromacs.org/mailing_lists/users.php
> >>>>
> >>>>
> >>>>>
> >>>>>
> >>>>>
> >>>> _______________________________________________
> >>>> gmx-users mailing list gmx-users at gromacs.org
> >>>>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>>> Please don't post (un)subscribe requests to the
> >>>> list. Use the
> >>>> www interface or send it to
> >>>> gmx-users-request at gromacs.org.
> >>>> Can't post? Read
> >>>> http://www.gromacs.org/mailing_lists/users.php
> >>>>
> >>>>
> >>>>
> >>>
> __________________________________________________
> >>> Do You Yahoo!?
> >>> Tired of spam? Yahoo! Mail has the best spam
> >>>
> >> protection around
>
=== message truncated ===
__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com
More information about the gromacs.org_gmx-users
mailing list