Dear All,
I am trying to simulate a enzyme-ligand complex where ligand is
cobalt-complex.I am trying to carry out DFTB type QMMM simulation.
I have also downloaded trans3d parameters from dftb and placed them in slko
directory. Now when I am trying to run qmm simulation keeping my ligand in
QM part Sander is treating Cobalt as carbon and Carrying out
simulation.This I came to know from log file where in QM region first atom
was show as carbon (part of output is pasted below) In prmtop file the atom
name of cobalt is mentioned as CO1 and amot type as Co.
Part of my prmtop is pated below
%FLAG ATOM_NAME
*CO1* N1 C1 H1 C2 H2 C3 H3 C4 C5 C6 N3 H3A N2 H2A C7 O1 N11
C11 H11 C21 H21
C31 H31 C41 C51 C61 N31 H3A1N21 H2A1C71 O11 N12 C12 H12 C22 H22 C32 H32 C42
C52
C62 N32 H3A2N22 H2A2C72 O12 N13 C13 H13 C23 H23 C33 H33 C43 C53 C63 N33
H3A3N23
H2A3C73 O13 N14 C14 H14 C24 H24 C34 H34 C44 C54 C64 N34 H3A4N24 H2A4C74 O14
N15
C15 H15 C25 H25 C35 H35 C45 C55 C65 N35 H3A5N25 H2A5C75 O15 O H1 H2 O
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
*Co* NA CA HA CA HA CA HA CA CA CT N H N H C O NA
CA HA CA HA
CA HA CA CA CT N H N H C O NA CA HA CA HA CA HA CA
CA
CT N H N H C O NA CA HA CA HA CA HA CA CA CT N H
N
H C O NA CA HA CA HA CA HA CA CA CT N H N H C O
NA
*output is pasted below where in output first atom should be cobalt where it
is being treated as C*
Output
QMMM: QM_NO. MM_NO. ATOM X Y Z
* QMMM: 1 8279 C -0.6382 -0.6715 0.9812*
QMMM: 2 8280 N 1.2731 -0.6218 -0.0952
QMMM: 3 8281 C 1.9976 0.3551 -0.8670
QMMM: 4 8282 H 1.5998 1.3182 -1.1764
QMMM: 5 8283 C 3.3121 0.2335 -1.2932
QMMM: 6 8284 H 3.7125 1.0319 -1.9127
QMMM: 7 8285 C 4.0161 -0.9201 -1.0509
QMMM: 8 8286 H 4.9968 -1.0257 -1.5078
QMMM: 9 8287 C 3.4570 -1.8830 -0.2573
QMMM: 10 8288 C 2.1485 -1.6992 0.2375
QMMM: 11 8289 C 4.2659 -3.1540 -0.0661
QMMM: 12 8290 N 5.5728 -2.8904 0.4947
QMMM: 13 8291 H 6.3540 -2.4813 0.0042
QMMM: 14 8292 N 4.3212 -3.8931 -1.3111
QMMM: 15 8293 H 4.3526 -3.4679 -2.2256
QMMM: 16 8294 C 5.8271 -3.5267 1.6237
QMMM: 17 8295 O 6.7660 -3.3274 2.3438
QMMM: 18 8296 N 0.2067 -2.5201 1.0981
QMMM: 19 8297 C -0.4168 -3.4512 1.9251
QMMM: 20 8298 H -1.4679 -3.3216 2.1703
Thanks and regards
vinod
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Received on Tue Oct 11 2011 - 06:00:02 PDT
