Hi David sir
Could you please help me in coming out of the above error?.
Highlights:
I am loading frcmod.ionsjc_tip3pfor monovalent ions, but still getting
error as:
Error: For atom (.R<Na+ 11808>.A<Na+ 1>) could not find vdW (or other)
parameters for type (IP)
Warning: Parameter file was not saved.
On Sun, Jul 14, 2019 at 9:20 AM shivangi agarwal <
shiviagarwalpharma.gmail.com> wrote:
> Ya sure
> I am attaching you leap log along with parameters and input files
>
> On Sat, Jul 13, 2019 at 10:25 AM Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
>
>> Could you send me your input files (including your coordinate files and
>> the
>> additional parameters you need to load) off the list?
>> Best Regards
>> Elvis Martis
>>
>>
>> On Sat, 13 Jul 2019 at 09:54, shivangi agarwal <
>> shiviagarwalpharma.gmail.com>
>> wrote:
>>
>> > Ya, that is what I am doing but getting other errors as mentioned above
>> >
>> > On Sat, Jul 13, 2019 at 9:52 AM Elvis Martis <elvis_bcp.elvismartis.in>
>> > wrote:
>> >
>> > > The hashed ones are NOT to be loaded in leap.
>> > >
>> > > On Saturday, July 13, 2019, shivangi agarwal <
>> > shiviagarwalpharma.gmail.com
>> > > >
>> > > wrote:
>> > >
>> > > > If I am correct, the hashed one I have to leave as per your
>> suggestion,
>> > > >
>> > > > tleap
>> > > > source leaprc.gaff
>> > > > source leaprc.protein.ff14SB
>> > > > loadAmberParams ligand.frcmod
>> > > > #loadoff atomic_ions.lib
>> > > > loadoff ligand.lib
>> > > > #loadAmberParams frcmod.ions234lm_iod_tip3p
>> > > >
>> > > > com=loadpdb complex_42_final_2_noH.pdb
>> > > > savepdb com see.pdb
>> > > > saveAmberParm com see.prmtop see.inpcrd
>> > > > source leaprc.water.tip3p
>> > > > solvateBox com TIP3PBOX 10.0
>> > > > charge com
>> > > > #loadoff ions94.lib
>> > > > addions com Na+ 6
>> > > > #loadamberparams frcmod.ionsjc_tip3p
>> > > > saveAmberParm com see.prmtop see.inpcrd
>> > > > savepdb com see-box.pdb
>> > > >
>> > > > But, when I am leaving out loadoff atomic_ions.lib, I am getting
>> > "FATAL:
>> > > > Atom .R<ZN 260>.A<ZN 1> does not have a type".
>> > > > and when I am leaving out #loadoff ions94.lib, Error: addIons:
>> Argument
>> > > #2
>> > > > is type String must be of type: [unit].
>> > > > I don't know what to do...
>> > > >
>> > > > On Sat, Jul 13, 2019 at 1:07 AM David Case <dacase1.gmail.com>
>> wrote:
>> > > >
>> > > > >
>> > > > > >
>> > > > > > tleap
>> > > > > > source leaprc.gaff
>> > > > > > source leaprc.protein.ff14SB
>> > > > > > loadAmberParams ligand.frcmod
>> > > > > > loadoff atomic_ions.lib
>> > > > >
>> > > > > Try leaving this out.
>> > > > >
>> > > > > > loadoff ligand.lib
>> > > > > > loadAmberParams frcmod.ions234lm_iod_tip3p
>> > > > >
>> > > > > Try leaving this out.
>> > > > >
>> > > > > > com=loadpdb complex_42_final_2_noH.pdb
>> > > > > > savepdb com see.pdb
>> > > > > > saveAmberParm com see.prmtop see.inpcrd
>> > > > > > source leaprc.water.tip3p
>> > > > > > solvateBox com TIP3PBOX 10.0
>> > > > > > charge com
>> > > > > > loadoff ions94.lib
>> > > > >
>> > > > > Ooh... leave this out...it is 25 years old.
>> > > > >
>> > > > > > addions com Na+ 6
>> > > > > > loadamberparams frcmod.ionsjc_tip3p
>> > > > >
>> > > > > Leave this out...it has already been loaded..
>> > > > >
>> > > > > > saveAmberParm com see.prmtop see.inpcrd
>> > > > > > savepdb com see-box.pdb
>> > > > > >
>> > > > > > saveAmberParm com see-box.inpcrd see-box.prmtop
>> > > > > You should use AmberTools19 if you are not doing so. Just load
>> one
>> > > > leaprc
>> > > > > for proteins, and one leaprc for ions
>> > > > >
>> > > > > ....dac
>> > > > > _______________________________________________
>> > > > > AMBER mailing list
>> > > > > AMBER.ambermd.org
>> > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > >
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org
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>> > > >
>> > >
>> > >
>> > > --
>> > > Best Regards
>> > > Elvis Martis
>> > > Mumbai.
>> > > _______________________________________________
>> > > AMBER mailing list
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>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
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>> >
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Received on Sun Jul 14 2019 - 23:30:02 PDT
