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#37292 - 01/18/19 10:09 AM NONE patch
pmj Offline
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Registered: 01/15/19
Posts: 46
Hello!

I am trying to apply no patch on the N-terminal residue,as I am missing the first 8 residues. Howeverm I get the error message that I am missing HN coordinates so that in the end they look like 9999.000 9999.000 9999.000.

When you apply NTER to the same case, it works like a charm.

I suppose I am just missing some keyword or I am not seeing the error. All in all, I would appreciate your help.

Thank you!


Attachments
build_test.txt (90 downloads)
chainA.txt (88 downloads)


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#37293 - 01/18/19 12:26 PM Re: NONE patch [Re: pmj]
rmv Offline

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Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
How do you plan to deal with the connectivity for the N atom? The AA residues are defined in the topology file with implied bonds to previous and next residues, so something must be done at the ends of the polymer chains to avoid problems. For the N-terminal residue, the ACE patch is commonly used for truncated sequences; it adds an acetyl group to create an amide, and satisfy connectivity w/o adding a + charge.
_________________________
Rick Venable
computational chemist


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#37294 - 01/23/19 03:13 AM Re: NONE patch [Re: rmv]
pmj Offline
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Registered: 01/15/19
Posts: 46
Dear Rick,

thank you for the replay. Actually, I thought to model the missing residues maybe or to apply some patch, it's just I did not know what is the common practice.

What about CTER then, which patch is common to use if you are missing the last residue? Also, in case you have nucleic acid and you are missing a residue on 5' and 3'-end, which patch you use?

Is there anywhere where I could read more about it? I am not sure I saw it in the official documentation, but there is a chance I just missed it in the end.

I would appreciate your answer.

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#37295 - 01/23/19 12:00 PM Re: NONE patch [Re: pmj]
rmv Offline

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Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
For the neutral case, I've typically used -NH-CH3 for the C-term, which is the CT3 patch.

If there are only a few residues missing at the ends, it is also reasonable and straightforward to include them and build the coordinates.

The standard patches are usually okay for nucleic acids, as they don't change the charge.
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Rick Venable
computational chemist


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#37296 - 01/24/19 03:01 AM Re: NONE patch [Re: pmj]
lennart Offline

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
The default terminal patches for nucleic acids are NONE, which is not OK. You have to specify whether you want a charged (-1) phosphate (5PHO, 3PHO) or a non-charged hydroxyl (5TER, 3TER) at either end; both exist in nature, so the user has to make the decision, and that is also why there is no default patch. One often wants to avoid having many charges so 5TER and 3TER are commonly used. In your case the phoshpate might be more appropriate. It is also quite easy to model a couple of missing nucleotides at the end.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#37297 - 01/24/19 04:17 AM Re: NONE patch [Re: pmj]
pmj Offline
Forum Member

Registered: 01/15/19
Posts: 46
Dear Rick and Lennart,

I really appreciate your answers. In the end I opted to apply 5PHO and 3PHO patches, but I was wondering which tools can one use to model nucleotides? I know for proteins I can use Modeller.

Thank you once more for your help!

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#37300 - 01/24/19 01:27 PM Re: NONE patch [Re: pmj]
rmv Offline

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Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
You should have a look at the Nucleic Acid MOdeling Tool at namot.sourceforge.net
_________________________
Rick Venable
computational chemist


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#37301 - 01/25/19 03:12 AM Re: NONE patch [Re: rmv]
pmj Offline
Forum Member

Registered: 01/15/19
Posts: 46
Dear Rick,

I will check Nucleic Acid MOdeling Tool. Thank you for all your answers.

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