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

[Justin Lemkul]

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

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