[gmx-users] C-terminus residue name in Gromos43a1

[Francesca Vitalini]

Residue 2 is just alanine,the most standard amino acid ever.

Any help?

Francesca.
 Il 26/feb/2014 11:58 "Justin Lemkul" <jalemkul at vt.edu> ha scritto:

>
>
> On 2/26/14, 4:08 AM, Francesca Vitalini wrote:
>
>> Dear Justin
>>
>>
>> 2014-02-25 19:07 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>>>
>>> On 2/25/14, 12:56 PM, Francesca Vitalini wrote:
>>>
>>>  Dear Justin,
>>>>
>>>> Thanks for your answer.
>>>> However I noticed that I had made a mistake and there is no definition
>>>> of
>>>> NAC in GROMOS53a6, it was the .rtp file of OPLS-AA I was looking at.
>>>>
>>>> So defining a new residue-type in the rtp file is not as trivial as I
>>>> had
>>>> hoped.
>>>> I followed the instructions given on the GROMACS wab page
>>>> http://www.gromacs.org/Documentation/How-tos/Adding_
>>>> a_Residue_to_a_Force_Field
>>>>
>>>> and copied the gromos43a1.ff folder and the residuetypes.dat file in my
>>>> local directory.
>>>> I have added the following definition of NAC to the
>>>> gromos43a1.ff/aminoacids.rtp file
>>>>
>>>> [ NAC ]
>>>>    [ atoms ]
>>>>           N     N    -0.28000     0
>>>>           H     H     0.28000     0
>>>>          CA   CH3     0.00000     0
>>>>    [ bonds ]
>>>>           N    CA    gb_20
>>>>           N     H    gb_2
>>>>
>>>>
>>> You're missing a bond here, from N to -C.
>>>
>>
>>
>> I hadn't add that as all the other residue types also don't have it
>> defined. It seems to me that the bond is defined as C to N+ not the other
>> way round. In this case however I have no N+ and the hydrogens are not
>> defined, so how can I properly define that bond?
>>
>> I also tried to define the bond N to -C as gb_9 (ie the bond type of C to
>> N+) but it leads to the exact same error message.
>>
>>
> Ah, true, this isn't necessary.
>
>
>>
>>>     [ angles ]
>>>
>>>> ;  ai    aj    ak   gromos type
>>>>          -C     N     H     ga_31
>>>>           H     N    CA     ga_17
>>>>          -C     N    CA     ga_30
>>>>    [ impropers ]
>>>> ;  ai    aj    ak    al   gromos type
>>>>       N    -C    CA     H     gi_1
>>>>    [ dihedrals ]
>>>> ;  ai    aj    ak    al   gromos type
>>>>     -CA    -C     N    CA     gd_4
>>>>
>>>> and then tried again the pdb2gmx command as following and obtained this
>>>> error
>>>> Fatal error:
>>>> There is a dangling bond at at least one of the terminal ends. Select a
>>>> proper terminal entry.
>>>> For more information and tips for troubleshooting, please check the
>>>> GROMACS
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>
>>>>
>>>> Evidently I have not defined correctly my NAC residue. However, I am not
>>>> sure of how to correctly define the bonds in this specific case. Could
>>>> you
>>>> possibly identify the error and/or point me where to find detailed
>>>> information? I have already looked at the manual but haven't been able
>>>> to
>>>> come up with successful definition.
>>>>
>>>>
>>>>  You need to use pdb2gmx -ter and select "None" for the C-terminus,
>>> otherwise pdb2gmx tries to build a carboxylate.  When it can't find the
>>> atoms it needs to do this, it fails.
>>>
>>>
>> I do use the -ter "None" option for both termini and the error is still
>> present. What I find interesting is this part of the pdb2gmx output
>>
>> Select start terminus type for ACE-1
>>   0: NH3+
>>   1: NH2
>>   2: None
>> 2
>> Start terminus ACE-1: None
>> Select end terminus type for ACE-1
>>   0: COO-
>>   1: COOH
>>   2: None
>> 2
>> End terminus ACE-1: None
>>
>>
>> where it looks like that ACE is the end terminus, not NAC, despite my pdb
>> looks like the following. Any suggestions?
>>
>>
> What is residue 2?  Is it anything non-standard?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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