VMD-L Mailing List

From: Manish Agarwal (zmanish_at_gmail.com)
Date: Tue Dec 04 2018 - 12:55:30 CST

NAMD tutorial files for MARTINI:
http://www.ks.uiuc.edu/Training/Tutorials/martini/
I guess it is buggy. I am not sure where I can get "new" versions. Any
suggestions?

Thanks,
Manish Agarwal
<zmanish_at_gmail.com>
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On Wed, Dec 5, 2018 at 12:21 AM Peter Freddolino <petefred_at_umich.edu> wrote:

> Yeah... that topology entry seems wonky, because it is listing in the BOND
> statement what appear to be atom TYPES (based on your psf snippet), but
> should in fact be atom NAMES. Where did you get this topology from?
> Thanks,
> Peter
>
> On Tue, Dec 4, 2018 at 11:54 AM Manish Agarwal <zmanish_at_gmail.com> wrote:
>
>> Do you mean the DISU entry in the martini-protein.top file?
>>
>> ! disulfide bond
>> PRES DISU 0.0
>> BOND 1C5c 2C5c
>>
>> Thanks,
>> Manish Agarwal
>> <zmanish_at_gmail.com>
>> - - - - - - - - - - - - - - - - - - - - - - - - - - -
>>
>>
>> On Tue, Dec 4, 2018 at 6:49 PM Peter Freddolino <petefred_at_umich.edu>
>> wrote:
>>
>>> What does the topology for your DISU patch entry look like?
>>> Best,
>>> Peter
>>>
>>> On Tue, Dec 4, 2018 at 4:10 AM Manish Agarwal <zmanish_at_gmail.com> wrote:
>>>
>>>> Dear VMD Users,
>>>> Context: using the NAMD MARTINI tutorial as a reference, I am trying to
>>>> martinize a dipeptide.
>>>>
>>>> I seem to be missing something very basic in trying to add a disulfide
>>>> bond/patch between two "martinized" protein segments. The two segments are
>>>> identical with one TRP and one CYS residues (only). Autopsf fails to add
>>>> the diulfide bond - the error is similar to the one when trying to update
>>>> the psf manually:
>>>>
>>>> topology martini-protein.top
>>>> readpsf cg-single.psf
>>>> coordpdb cg-single.pdb
>>>> patch DISU P1:1 P2:1
>>>> psfgen) applying patch DISU to 2 residues
>>>> psfgen) no atom C5C in residue CYS:1 of segment P1
>>>> psfgen) Warning: add bond failed in patch DISU
>>>>
>>>> The "sulfur" in the CYS residue has "C5c" _type_ ; the name is SID. Is
>>>> case sensitivity an issue?
>>>> Excerpt from the psf:
>>>> 14 !NATOM
>>>> 1 P1 1 CYS BAS P5 0.000000 72.0000 0
>>>> 2 P1 1 CYS SID C5c 0.000000 72.0000 0
>>>> 3 P1 2 TRP BAS P5 0.000000 72.0000 0
>>>> 4 P1 2 TRP SI1 SC4w 0.000000 45.0000 0
>>>> 5 P1 2 TRP SI2 SP1w 0.000000 45.0000 0
>>>> 6 P1 2 TRP SI3 SC4w 0.000000 45.0000 0
>>>> 7 P1 2 TRP SI4 SC4w 0.000000 45.0000 0
>>>> 8 P2 1 CYS BAS P5 0.000000 72.0000 0
>>>> 9 P2 1 CYS SID C5c 0.000000 72.0000 0
>>>> 10 P2 2 TRP BAS P5 0.000000 72.0000 0
>>>> 11 P2 2 TRP SI1 SC4w 0.000000 45.0000 0
>>>> 12 P2 2 TRP SI2 SP1w 0.000000 45.0000 0
>>>> 13 P2 2 TRP SI3 SC4w 0.000000 45.0000 0
>>>> 14 P2 2 TRP SI4 SC4w 0.000000 45.0000 0
>>>>
>>>> Any suggestions/directions are welcome.
>>>>
>>>> Thanks,
>>>> Manish Agarwal
>>>> <zmanish_at_gmail.com>
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>>>>
>>>