VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Dec 04 2018 - 12:54:13 CST

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