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

[yuemin liu]

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 ===



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