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Patches and cofactors in charmm #3
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Adreasing your last point, I'm not confident that parametrise in its
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We have done it already
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Which 'it'?
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I added CHARMM stream files in the new multiscalelab/htmd. Do |
Fantastic!! I just saw it. |
Yes, it splits them into some temp files and then copies them into your On Tue, Apr 5, 2016 at 6:17 PM, Noelia Ferruz notifications@github.com
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pratically they are usable directly by charmmBuilt On 5 April 2016 at 19:18, Stefan notifications@github.com wrote:
https://www.youtube.com/user/acelleracom |
Can this be closed @noeliaferruz ? |
Hola! Sorry, I hadn't quite tested it. I have just tried to build the case with the phosphate patch. It's nothing important, I'm just trying to see if I can actually build a system with phosphates. These are the lines I'm using:
Visual inspection reveals that the phosphate is still there. I know @stefdoerr fixed this exact issue in Molecule.py some weeks ago, so I don't know. So, no don't close it yet, I'd like to find a way to add phosphates and other cofactors! Thanks, |
No, I think the issue was that VMD atomselect was recognizing phosphates as "protein". Seems to be the case here at least. I don't know a fix for that, other than making your autoSegment atomselection fancier to exclude the phosphates. |
But its mutateResidue who's not removing the entire sidechain of PTR, no? |
Ah if that's the case (which should be fixed), just swap the order. First do stuff like mutating etc and then autoSegment. Even if the phosphates are not removed (which they should), they will not be bonded any more to the protein so then the autoSegment should work correct. |
You are sure the phosphates belong to the old PTR residues? |
Ok, I'll do that. |
Wow. That means that the VMD atomselection recognizes those atoms as backbone. Can you verify that? Because I remove all atoms with |
Maybe this could be sent to the VMD mailing list? On Thu, Apr 21, 2016 at 6:08 PM, Noelia Ferruz notifications@github.com
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Kill me... :P Well that is somehow beyond my capabilities, haha. If anyone can find a generalized atomselect (that works on all residues) and removes them I will implement it. |
Yeah we could try our luck there. @noeliaferruz can you send the residue (and maybe one or two before and after for "context") by mail so that I can ask them? |
The backbone atoms are always N CA C O, no? |
I follow their mailing list, it's quite active. On Thu, Apr 21, 2016 at 6:13 PM, Stefan notifications@github.com wrote:
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Hm Noelia, the protein structure was it by any chance written by HTMD at some point? We had a small very weird issue with the PDB writer. Can you send me like the original original pdb structure of this residue? |
Apparently in the PDB format there is a significance on where you put atom names. So carbon alphas should be written in columns 13-16 as "..CA" but calcium should be ".CA." where dots indicate spaces. So if VMD assigns significance to that it could have problems. |
The original pdb: 5hx8.pdb ** But I'm using the first for the selections in the picture ** |
Ok thanks. It's not our error. Happens also if you get the PDB from the PDB website directly. Will ask the VMD mailing list. |
Would in the meanwhile |
yes, do it manually. Do |
yep. |
Ok apparently |
Maybe create a new selection protein-backbone instead of substitution? |
There is no such atomselection in VMD. I don't think I can invent atomselection shortcuts either. |
Not without modifying the VMD source code at least which I don't see as a real need. It would end up doing the same thing anyways. |
forget about it. you were talking about your specific application not HTMD On Fri, Apr 22, 2016 at 11:43 AM, Stefan notifications@github.com wrote:
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let's talk about it when Noelia is in BCN |
@noeliaferruz, let's see this on monday. |
we fixed this when Noelia was here, but now there's only a general problem with patching that's getting solved (#97) |
So we can close this then. All issues are fixed for this as far as I can see (atom naming, backbone selections) |
yes, only issue 97 left. |
Hello guys,
I am not finding an easy way to add patches or parameterize cofactors whose parameters are included in charmm already (like phosphates (TP2), hemoglobine (HEME), INO1.. etc)
The problem comes from the fact that these RESIs are (only) included in the charmm_27prot_na ff. This has two consequences:
I was wondering if this workaround in 2), which is error-prone and requires a lot of manual intervention could be easily handled with htmd. Phosphates, hemoglobines and other molecules are present in everyday simulations.
The other question is if these RESIs wouldnt be better described with parameterise.
Let me know what you think.
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