[AMBER] cpptraj H-bond: clarification sought

From: George Tzotzos <gtzotzos.me.com>
Date: Fri, 06 Mar 2015 14:44:55 -0300

Iím dealing homodimer complexed with two identical ligands named OVA and OVB (residues 126 and 252, respectively)

H-bond analysis based on the script:

parm 4fqt_solv.prmtop
trajin prod_0-100ns.nc
hbond H1 nointramol :126,252 series out Nhbond.agr avgout avg.dat bridgeout Bridge.dat solventdonor :WAT solventacceptor :WAT.O
go
write solutehb.agr H1[solutehb]
runanalysis lifetime H1[solutehb] out lifehb.agr window 10

produced the output as shown below:

#Acceptor DonorH Donor Frames Frac AvgDist AvgAng
#Solute-Solvent Hbonds:
#Acceptor DonorH Donor Count Frac AvgDist AvgAng
0VA_126.O9 SolventH SolventDnr 70 0.0070 2.8222 158.5911
0VB_252.O9 SolventH SolventDnr 23 0.0023 2.8135 159.6897

Using a script identical to the above but omitting the masked residues produced h-bonds for the ligand residues as shown below (indicative lines of output):

0VA_126.O9 TRP_114.HE1 TRP_114.NE1 734 0.0734 2.8660 149.4472
0VA_126.O9 PHE_123.H PHE_123.N 541 0.0541 2.9023 155.0698
0VA_126.O9 SolventH SolventDnr 70 0.0070 2.8222 158.5911
0VB_252.O9 TRP_240.HE1 TRP_240.NE1 1423 0.1423 2.8591 153.9400
0VB_252.O9 SolventH SolventDnr 23 0.0023 2.8135 159.6897

My question is why does the script above (ligand mask included) produce h-bonds with the solvent only but now with Trp114, Phe123 and Trp240?

Thank you in advance for any comments/suggestions

Regards

George


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Received on Fri Mar 06 2015 - 10:00:02 PST
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