VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Dec 04 2018 - 14:06:47 CST

I would reword that bond line to
BOND 1SID 2SID
You may also want to consider whether the atom types should change...
Best,
Peter

On Tue, Dec 4, 2018 at 1:55 PM Manish Agarwal <zmanish_at_gmail.com> wrote:

> 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>
> - - - - - - - - - - - - - - - - - - - - - - - - - - -
>
>
> 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>
>>>>> - - - - - - - - - - - - - - - - - - - - - - - - - - -
>>>>>
>>>>