VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Dec 04 2018 - 07:22:26 CST

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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