[gmx-users] Error when adding a unnatural amio acid
Yang Ye
leafyoung81-group at yahoo.com
Thu Jan 4 06:20:29 CET 2007
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 <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
> _______________________________________________
> 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
>
>
More information about the gromacs.org_gmx-users
mailing list