Dear David
I was performed MD simulations with perturbation by using force field you
recommended (ff03, ff02r1 and ff03ua ), but unfortunately they produced the
same result ( before saving the prmtop file with the use of the
"SaveAmberParmpert" command in xLeaP, I confirmed the bond information with
the "desc" command, and then, I saved the topology file. But, the bond
information was not held for the perturbed water molecule in the topology
file )
the topology and coordinate files were established by using the following
commands;
> source leaprc.ff03
> loadamberparams frcmod.tip5p
> MTP = copy TP5
> edit MTP (and then, I made the perturbation changes, and checked
with "desc" that the MTP unit has the proper bonds.)
> saveoff MTP mtp.off
> solvatebox MTP TP5 20.0 0.8
> saveAmberParmpert TMP parmpert.top parmpert.crd quit
> source leaprc.ff03ua
> loadamberparams frcmod.tip5p
> MTP = copy TP5
> edit MTP (and then, I made the perturbation changes, and checked
with "desc" that the MTP unit has the proper bonds.)
> saveoff MTP mtp.off
> solvatebox MTP TP5 20.0 0.8
> saveAmberParmpert TMP parmpert.top parmpert.crd quit
> source leaprc.ff02r1
> loadamberparams frcmod.tip5p
> MTP = copy TP5
> edit MTP (and then, I made the perturbation changes, and checked
with "desc" that the MTP unit has the proper bonds.)
> saveoff MTP mtp.off
> solvatebox MTP TP5 20.0 0.8
> saveAmberParmpert TMP parmpert.top parmpert.crd quit
Thanks in advanced.
Best wishes,
Sugino
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Received on Wed Jan 17 2007 - 06:08:25 PST
