From: Manish Agarwal (zmanish_at_gmail.com)
Date: Tue Dec 04 2018 - 10:54:14 CST

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>
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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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>>
>