[gmx-users] Residue not found in topology

Justin Lemkul jalemkul at vt.edu
Thu Aug 23 14:00:58 CEST 2018 


On 8/23/18 6:30 PM, Amir Zeb wrote:
> Thanks Justin,
>
> Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/  and
> generated the parameters for KAC.

Do not generate parameters in this way. You will have a mixture of 
highly optimized protein parameters for all other residues, then the 
CGenFF version of KAC. CGenFF parameters are inherently a trade-off 
between optimization and transferability. You'll also end up with a 
hodge-podge of bonded parameters that will need to be added and/or 
reoptimized to link this residue to its neighbors.

Please follow what I said before and create a proper .rtp entry. It is 
quite simple.

> 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?

You need to create an .hdb entry for the new residue.

-Justin

> 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
>>>>>
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>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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-- 
==================================================

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

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

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