AMBER Archive (2009)

Subject: [AMBER] Adding non standard residues

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Mon May 11 2009 - 03:54:25 CDT

Hi all,

I am trying to modify a water molecule and a cysteine residue from a crystal
structure - the two residues should be bonded to a nickel ion. I go through
tutorial 4 "*Simulating a Solvated Protein that Contains Non-Standard
Residues" *and create the cysteine residue from CYX to CYY and the water
from WAT to HOC residue names and save the two lib files

!!index array str
 "HOC"
!entry.HOC.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg
 "O" "OW" 0 1 131075 1 8 -0.614000
 "H1" "HW" 0 1 131075 2 1 0.445000
 "H2" "HW" 0 1 131075 3 1 0.445000
!entry.HOC.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
 "O" "OW" 0 -1 0.0
 "H1" "HW" 0 -1 0.0
 "H2" "HW" 0 -1 0.0
!entry.HOC.unit.boundbox array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.HOC.unit.childsequence single int
 336
!entry.HOC.unit.connect array int
 0
 0
!entry.HOC.unit.connectivity table int atom1x int atom2x int flags
 1 2 1
 1 3 1
!entry.HOC.unit.hierarchy table str abovetype int abovex str belowtype
int belowx
 "U" 0 "R" 1
 "R" 1 "A" 1
 "R" 1 "A" 2
 "R" 1 "A" 3
!entry.HOC.unit.name single str
 ""
!entry.HOC.unit.positions table dbl x dbl y dbl z
 16.313000 -9.193000 8.698000
 17.270000 -9.193000 8.698000
 16.073000 -8.266000 8.698000
!entry.HOC.unit.residueconnect table int c1x int c2x int c3x int c4x
int c5x int c6x
 0 0 0 0 0 0
!entry.HOC.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
 "HOC" 335 4 1 "?" 0
!entry.HOC.unit.residuesPdbSequenceNumber array int
 1
!entry.HOC.unit.solventcap array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.HOC.unit.velocities table dbl x dbl y dbl z
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0

and the cyy.lib file

!!index array str
 "CYY"
!entry.CYY.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg
 "N" "N" 0 1 131075 1 7 -0.416000
 "H" "H" 0 1 131075 2 1 0.272000
 "CA" "CT" 0 1 131075 3 6 0.097000
 "HA" "H1" 0 1 131075 4 1 0.112000
 "C" "C" 0 1 131075 5 6 0.597000
 "O" "O" 0 1 131075 6 8 -0.568000
 "CB" "CT" 0 1 131075 7 6 -0.059000
 "HB3" "H1" 0 1 131075 8 1 0.076000
 "HB2" "H1" 0 1 131075 9 1 0.076000
 "SG" "SJ" 0 1 131075 10 16 -0.284000
!entry.CYY.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
 "N" "N" 0 -1 0.0
 "H" "H" 0 -1 0.0
 "CA" "CT" 0 -1 0.0
 "HA" "H1" 0 -1 0.0
 "C" "C" 0 -1 0.0
 "O" "O" 0 -1 0.0
 "CB" "CT" 0 -1 0.0
 "HB3" "H1" 0 -1 0.0
 "HB2" "H1" 0 -1 0.0
 "SG" "SJ" 0 -1 0.0
!entry.CYY.unit.boundbox array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.CYY.unit.childsequence single int
 131
!entry.CYY.unit.connect array int
 1
 5
!entry.CYY.unit.connectivity table int atom1x int atom2x int flags
 1 3 1
 1 2 1
 3 5 1
 3 4 1
 3 7 1
 5 6 1
 7 9 1
 7 8 1
 7 10 1
!entry.CYY.unit.hierarchy table str abovetype int abovex str belowtype
int belowx
 "U" 0 "R" 1
 "R" 1 "A" 1
 "R" 1 "A" 2
 "R" 1 "A" 3
 "R" 1 "A" 4
 "R" 1 "A" 5
 "R" 1 "A" 6
 "R" 1 "A" 7
 "R" 1 "A" 8
 "R" 1 "A" 9
 "R" 1 "A" 10
!entry.CYY.unit.name single str
 ""
!entry.CYY.unit.positions table dbl x dbl y dbl z
 37.225000 1.282000 -4.799000
 36.565000 1.870000 -5.288000
 37.924000 0.174000 -5.486000
 38.090000 -0.623000 -4.792000
 39.260000 0.683000 -5.992000
 39.378000 1.901000 -6.241000
 36.989000 -0.307000 -6.590000
 36.712000 0.541000 -7.187000
 36.113000 -0.721000 -6.129000
 37.691000 -1.551000 -7.676000
!entry.CYY.unit.residueconnect table int c1x int c2x int c3x int c4x
int c5x int c6x
 0 0 0 0 0 0
!entry.CYY.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
 "CYY" 1 11 1 "?" 0
!entry.CYY.unit.residuesPdbSequenceNumber array int
 1
!entry.CYY.unit.solventcap array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.CYY.unit.velocities table dbl x dbl y dbl z
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0

This gives me two problems - first of all the HW-HW is not recognized by
NAMD is that because it is included in the new residue? The HOC residue
should be like any water molecule except that it is coordinated to Ni2+ ion
with the bond
BOND
NI-SG 101.62 2.18
ANGLE
NB-NI-SG 14.21 103.12

and the dihedrals are set to zero. Furthermore, when generating a prm or a
new pdb file the CYY residue is also added a TER and I get the following
message from xleap

Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

    res total affected

    CARG 1
    CYY 1
    HOC 1
    NGLN 1
    WAT 350
  )
 (no restraints)

for HOC it is ok but I presume this is not ok for CYY which is within the
protein chain? How to resolve these problems thanks in advance

Best regards

Jorgen
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