[gmx-users] Error when adding a unnatural amio acid

[Tsjerk Wassenaar]

Hi Liu Yeumin,

Maybe you can attach the .rtp building block, the .pdb file and the
.hdb file. This will make it easier to help you.

Cheers,

Tsjerk

On 1/4/07, yuemin liu <liucan1 at yahoo.com> wrote:
> I got it! The reasons are probably two. One is that
> the numbers assigned (like how many and how H to be
> added) in hdb file are not right. Secondly, the group
> number from prodrg should be left what they are. Happy
> thing is your being able to solve problems, unhappy
> one is that you can not solve all of them. Here I have
> new one: "WARNING: atom CB is missing in residue ASO 1
> in the pdb file". Maybe I should not show this one.
> But it is interesting. I have CB in rtp, hdb, and pdb
> file with correct format. I even adjust both C-C bonds
> of CB from 1.54 to 1.53. But it is still complaining.
>
> Thanks,
>
> Liu, Yuemin
>
> --- Yang Ye <leafyoung81-group at yahoo.com> wrote:
>
> > Please email me offline 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 <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
> >
> === message truncated ===
>
>
>
> __________________________________________________
> 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
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623