Dear Prof. Case,
First, thanks for your reply,
Secondly, sorry for my ignorance!
If I understand you correctly, you advise that I run a single tleap
script like this:
source leaprc.ff02EP
loadamberparams frcmod.pol3
WAT = PL3
prot = loadpdb xrayH.pdb
solvatebox WAT 10
addions2 prot Na+ 0
savamberparmpol prot prot.parm7 prot.crd
quit
This, of course gives a periodically repeating array of PL3 water molecules,
rather than the periodically repeating equilibrated water system (such
as WATBOX216 which is only for TIP3P).
I suppose the water molecules will equilibrate quickly during the
equilibration at 300K and changing
the density to 1. I always thought it was better to start with a
pre-equilibrated water box (such as WATBOX216).
I have two other short questions:
1. Is it somehow possible to strip the 1EP+ and 1EP- 'atoms' (in ptraj
for example)
when going to further analysis of the trajectory? Many of the anlysis
programs that
I have written or use get confused by these extra 'atoms'. I tried
stripping the atoms in
ptraj using 'strip 1EP+', like 'strip :WAT', but this didn't work.
2. If one wants to put re/constraints on atoms in a system,
such as cartesian constraints or a TMD restraint, should one include
these extra
point charges in the constrained group? For example, if one wants to put
constraints on
a backbone O atom, should one also apply a similar constraint to the
1EP+/1EP- charges
associated with this atom, or are these point charges that mimic the
lone-pair of electrons
rigidly attached to their respective atom (such as in a united atom
force-field)?
many thanks once again for all your help,
with best regards,
Phineus.
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Received on Mon Apr 04 2005 - 13:53:01 PDT
