[gmx-users] Residue not found in topology

Justin Lemkul jalemkul at vt.edu
Thu Aug 23 14:01:43 CEST 2018 


On 8/23/18 7:52 AM, Bratin Kumar Das wrote:
> Hi
>     You can see that only the problem is coming from hydrogen. So in pdb2gmx
> command use -ignh so that it ignores the hydrogen. If you use this this
> WARNING will not come.

That's not true. The -ignh option ignores H atoms in the input 
coordinate file and is useful when there are H atoms with names that do 
not agree with what is specified in the .rtp entry for the given 
residue. The OP's problem is the opposite: the H are not there but need 
to be built.

-Justin

> On Fri, Aug 24, 2018 at 4:00 AM, Amir Zeb <zebamir85 at gmail.com> wrote:
>
>> Thanks Justin,
>>
>> Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/  and
>> generated the parameters for KAC.
>> The merged.rtp file was modified by adding the KAC parameters
>> That issue fixed, but now I'm getting the following warning which
>> ultimately results in fatal error.
>>
>> WARNING: atom HA is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HA to the hydrogen database of building
>> block KAC
>>           in the file merged.hdb (see the manual)
>>
>>
>> WARNING: atom HB1 is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HB1 to the hydrogen database of
>> building block KAC
>>           in the file merged.hdb (see the manual)
>>
>>
>> WARNING: atom HB2 is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HB2 to the hydrogen database of
>> building block KAC
>>           in the file merged.hdb (see the manual)
>>
>>
>> WARNING: atom HG1 is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HG1 to the hydrogen database of
>> building block KAC
>>           in the file merged.hdb (see the manual)
>>
>>
>> WARNING: atom HG2 is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HG2 to the hydrogen database of
>> building block KAC
>>           in the file merged.hdb (see the manual)
>>
>>
>> WARNING: atom HD1 is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HD1 to the hydrogen database of
>> building block KAC
>>           in the file merged.hdb (see the manual)
>>
>>
>> WARNING: atom HD2 is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HD2 to the hydrogen database of
>> building block KAC
>>           in the file merged.hdb (see the manual)
>>
>>
>> WARNING: atom HE1 is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HE1 to the hydrogen database of
>> building block KAC
>>           in the file merged.hdb (see the manual)
>>
>>
>> WARNING: atom HE2 is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HE2 to the hydrogen database of
>> building block KAC
>>           in the file merged.hdb (see the manual)
>>
>>
>> WARNING: atom HZ1 is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HZ1 to the hydrogen database of
>> building block KAC
>>           in the file merged.hdb (see the manual)
>>
>>
>> WARNING: atom HI11 is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HI11 to the hydrogen database of
>> building block KAC
>>           in the file merged.hdb (see the manual)
>>
>>
>> WARNING: atom HI12 is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HI12 to the hydrogen database of
>> building block KAC
>>           in the file merged.hdb (see the manual)
>>
>>
>> WARNING: atom HI13 is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HI13 to the hydrogen database of
>> building block KAC
>>           in the file merged.hdb (see the manual)
>>
>>
>> WARNING: atom HZ2 is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HZ2 to the hydrogen database of
>> building block KAC
>>           in the file merged.hdb (see the manual)
>>
>>
>> WARNING: atom HT2 is missing in residue KAC 33 in the pdb file
>>           You might need to add atom HT2 to the hydrogen database of
>> building block KAC
>>           in the file merged.hdb (see the manual)
>>
>> How may I fix this issue?
>>
>> Thanks in advance!
>>
>>
>> On Wed, Aug 22, 2018 at 4:31 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>> On 8/22/18 5:26 AM, Bratin Kumar Das wrote:
>>>> Hi
>>>>       In your tool.top file the particular lys molecule residue name you
>>> have
>>>> to modify. Then it will work..Actually grompp can't find the molecule
>> in
>>>> the topology.
>>> The error has nothing to do with grompp. The topology was never created
>>> because pdb2gmx could not write a topology for KAC.
>>>
>>> CHARMM36 does support KAC, but not as a standalone residue. In CHARMM,
>>> one would generate a normal lysine then patch it with the KAC patch. To
>>> make this work in GROMACS, one would have to create a KAC .rtp entry by
>>> applying the same logic - modify LYS according to the KAC patch (found
>>> in the stream/prot/toppar_all36_prot_modify_res.str file from the
>>> tarball distributed by Alex MacKerell:
>>> http://mackerell.umaryland.edu/charmm_ff.shtml#charmm).
>>>
>>> -Justin
>>>
>>>> On Wed 22 Aug, 2018, 2:53 PM Bratin Kumar Das, <
>>> 177cy500.bratin at nitk.edu.in>
>>>> wrote:
>>>>
>>>>> Hi
>>>>>       In your tool.top file the particular lys molecule residue name
>> you
>>>>> have to modify. Then it will work..Actually grompp can't find the
>>> molecule
>>>>> in the topology.
>>>>>
>>>>> On Wed 22 Aug, 2018, 11:35 AM Amir Zeb, <zebamir85 at gmail.com> wrote:
>>>>>
>>>>>> Hi gromacs users,
>>>>>>
>>>>>> I want to simulate a protein where one of the lysine residues is
>>> modified
>>>>>> to acetylated lysine and has been denoted by KAC. I want to simulate
>>> it by
>>>>>> CharmM 36 ff, but it gave me this error.
>>>>>>
>>>>>>
>>>>>> Program gmx pdb2gmx, VERSION 5.1.4
>>>>>> Source code file:
>>>>>> /home/chip/Downloads/gromacs-5.1.4/src/gromacs/
>> gmxpreprocess/resall.c,
>>>>>> line: 645
>>>>>>
>>>>>> Fatal error:
>>>>>> Residue 'KAC' not found in residue topology database
>>>>>> For more information and tips for troubleshooting, please check the
>>>>>> GROMACS
>>>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>>>
>>>>>>
>>>>>> Is CharmM 36 ff capable to simulate modified residue acetylated
>> lysine?
>>>>>> If yes, what is the ff compatible notation for acetylated lysine?
>>>>>> If not, which ff can I use to simulate acetylated lysine?
>>>>>>
>>>>>> Thanks in advance!
>>>>>>
>>>>>> Amir
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================

More information about the gromacs.org_gmx-users mailing list