VMD-L Mailing List

From: Manish Agarwal (zmanish_at_gmail.com)
Date: Tue Dec 04 2018 - 01:45:08 CST

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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