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From: Saeed Nasiri <s.t.nasiri.gmail.com>

Date: Mon, 2 Dec 2013 19:55:22 +0330

Dear All

I have a problem with ionic liquid simulation tutorial.

It seems that there is problem with saving "amberparameters" command in

tleap for simulation box (5 Using tLEaP to generate Amber prmtop file).

I tested that with saving parameters for a box of acetonitrile molecules

only with the tutorial method and all things are right; I repeated for BMI

and BF4 ions but the "atom type error" appeared and I don't know why?

Also after loading parameters from frcmod file in tleap for BMI and BF4 I

check the ions parameters in tleap and there was no problem but it could

not save parameters for box?

Thanks

.

.

.

FATAL: Atom .R<bf4 98>.A<B1 1> does not have a type.

FATAL: Atom .R<bf4 98>.A<F2 2> does not have a type.

FATAL: Atom .R<bf4 98>.A<F3 3> does not have a type.

FATAL: Atom .R<bf4 98>.A<F4 4> does not have a type.

FATAL: Atom .R<bf4 98>.A<F5 5> does not have a type.

FATAL: Atom .R<bf4 99>.A<B1 1> does not have a type.

FATAL: Atom .R<bf4 99>.A<F2 2> does not have a type.

FATAL: Atom .R<bf4 99>.A<F3 3> does not have a type.

FATAL: Atom .R<bf4 99>.A<F4 4> does not have a type.

FATAL: Atom .R<bf4 99>.A<F5 5> does not have a type.

FATAL: Atom .R<bf4 100>.A<B1 1> does not have a type.

FATAL: Atom .R<bf4 100>.A<F2 2> does not have a type.

FATAL: Atom .R<bf4 100>.A<F3 3> does not have a type.

FATAL: Atom .R<bf4 100>.A<F4 4> does not have a type.

FATAL: Atom .R<bf4 100>.A<F5 5> does not have a type.

FATAL: Atom .R<bf4 101>.A<B1 1> does not have a type.

FATAL: Atom .R<bf4 101>.A<F2 2> does not have a type.

FATAL: Atom .R<bf4 101>.A<F3 3> does not have a type.

FATAL: Atom .R<bf4 101>.A<F4 4> does not have a type.

FATAL: Atom .R<bf4 101>.A<F5 5> does not have a type.

FATAL: Atom .R<bf4 102>.A<B1 1> does not have a type.

FATAL: Atom .R<bf4 102>.A<F2 2> does not have a type.

FATAL: Atom .R<bf4 102>.A<F3 3> does not have a type.

FATAL: Atom .R<bf4 102>.A<F4 4> does not have a type.

FATAL: Atom .R<bf4 102>.A<F5 5> does not have a type.

Failed to generate parameters

Parameter file was not saved.

.

.

.

.

FATAL: Atom .R<bmi 101>.A<H16 16> does not have a type.

FATAL: Atom .R<bmi 101>.A<H17 17> does not have a type.

FATAL: Atom .R<bmi 101>.A<H18 18> does not have a type.

FATAL: Atom .R<bmi 101>.A<H19 19> does not have a type.

FATAL: Atom .R<bmi 101>.A<H20 20> does not have a type.

FATAL: Atom .R<bmi 101>.A<H21 21> does not have a type.

FATAL: Atom .R<bmi 101>.A<H22 22> does not have a type.

FATAL: Atom .R<bmi 101>.A<H23 23> does not have a type.

FATAL: Atom .R<bmi 101>.A<H24 24> does not have a type.

FATAL: Atom .R<bmi 101>.A<H25 25> does not have a type.

FATAL: Atom .R<bmi 102>.A<C1 1> does not have a type.

FATAL: Atom .R<bmi 102>.A<N2 2> does not have a type.

FATAL: Atom .R<bmi 102>.A<N3 3> does not have a type.

FATAL: Atom .R<bmi 102>.A<C4 4> does not have a type.

FATAL: Atom .R<bmi 102>.A<C5 5> does not have a type.

FATAL: Atom .R<bmi 102>.A<C6 6> does not have a type.

FATAL: Atom .R<bmi 102>.A<C7 7> does not have a type.

FATAL: Atom .R<bmi 102>.A<C8 8> does not have a type.

FATAL: Atom .R<bmi 102>.A<C9 9> does not have a type.

FATAL: Atom .R<bmi 102>.A<C10 10> does not have a type.

FATAL: Atom .R<bmi 102>.A<H11 11> does not have a type.

FATAL: Atom .R<bmi 102>.A<H12 12> does not have a type.

FATAL: Atom .R<bmi 102>.A<H13 13> does not have a type.

FATAL: Atom .R<bmi 102>.A<H14 14> does not have a type.

FATAL: Atom .R<bmi 102>.A<H15 15> does not have a type.

FATAL: Atom .R<bmi 102>.A<H16 16> does not have a type.

FATAL: Atom .R<bmi 102>.A<H17 17> does not have a type.

FATAL: Atom .R<bmi 102>.A<H18 18> does not have a type.

FATAL: Atom .R<bmi 102>.A<H19 19> does not have a type.

FATAL: Atom .R<bmi 102>.A<H20 20> does not have a type.

FATAL: Atom .R<bmi 102>.A<H21 21> does not have a type.

FATAL: Atom .R<bmi 102>.A<H22 22> does not have a type.

FATAL: Atom .R<bmi 102>.A<H23 23> does not have a type.

FATAL: Atom .R<bmi 102>.A<H24 24> does not have a type.

FATAL: Atom .R<bmi 102>.A<H25 25> does not have a type.

Failed to generate parameters

Parameter file was not saved.

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Dec 02 2013 - 08:30:02 PST

Date: Mon, 2 Dec 2013 19:55:22 +0330

Dear All

I have a problem with ionic liquid simulation tutorial.

It seems that there is problem with saving "amberparameters" command in

tleap for simulation box (5 Using tLEaP to generate Amber prmtop file).

I tested that with saving parameters for a box of acetonitrile molecules

only with the tutorial method and all things are right; I repeated for BMI

and BF4 ions but the "atom type error" appeared and I don't know why?

Also after loading parameters from frcmod file in tleap for BMI and BF4 I

check the ions parameters in tleap and there was no problem but it could

not save parameters for box?

Thanks

.

.

.

FATAL: Atom .R<bf4 98>.A<B1 1> does not have a type.

FATAL: Atom .R<bf4 98>.A<F2 2> does not have a type.

FATAL: Atom .R<bf4 98>.A<F3 3> does not have a type.

FATAL: Atom .R<bf4 98>.A<F4 4> does not have a type.

FATAL: Atom .R<bf4 98>.A<F5 5> does not have a type.

FATAL: Atom .R<bf4 99>.A<B1 1> does not have a type.

FATAL: Atom .R<bf4 99>.A<F2 2> does not have a type.

FATAL: Atom .R<bf4 99>.A<F3 3> does not have a type.

FATAL: Atom .R<bf4 99>.A<F4 4> does not have a type.

FATAL: Atom .R<bf4 99>.A<F5 5> does not have a type.

FATAL: Atom .R<bf4 100>.A<B1 1> does not have a type.

FATAL: Atom .R<bf4 100>.A<F2 2> does not have a type.

FATAL: Atom .R<bf4 100>.A<F3 3> does not have a type.

FATAL: Atom .R<bf4 100>.A<F4 4> does not have a type.

FATAL: Atom .R<bf4 100>.A<F5 5> does not have a type.

FATAL: Atom .R<bf4 101>.A<B1 1> does not have a type.

FATAL: Atom .R<bf4 101>.A<F2 2> does not have a type.

FATAL: Atom .R<bf4 101>.A<F3 3> does not have a type.

FATAL: Atom .R<bf4 101>.A<F4 4> does not have a type.

FATAL: Atom .R<bf4 101>.A<F5 5> does not have a type.

FATAL: Atom .R<bf4 102>.A<B1 1> does not have a type.

FATAL: Atom .R<bf4 102>.A<F2 2> does not have a type.

FATAL: Atom .R<bf4 102>.A<F3 3> does not have a type.

FATAL: Atom .R<bf4 102>.A<F4 4> does not have a type.

FATAL: Atom .R<bf4 102>.A<F5 5> does not have a type.

Failed to generate parameters

Parameter file was not saved.

.

.

.

.

FATAL: Atom .R<bmi 101>.A<H16 16> does not have a type.

FATAL: Atom .R<bmi 101>.A<H17 17> does not have a type.

FATAL: Atom .R<bmi 101>.A<H18 18> does not have a type.

FATAL: Atom .R<bmi 101>.A<H19 19> does not have a type.

FATAL: Atom .R<bmi 101>.A<H20 20> does not have a type.

FATAL: Atom .R<bmi 101>.A<H21 21> does not have a type.

FATAL: Atom .R<bmi 101>.A<H22 22> does not have a type.

FATAL: Atom .R<bmi 101>.A<H23 23> does not have a type.

FATAL: Atom .R<bmi 101>.A<H24 24> does not have a type.

FATAL: Atom .R<bmi 101>.A<H25 25> does not have a type.

FATAL: Atom .R<bmi 102>.A<C1 1> does not have a type.

FATAL: Atom .R<bmi 102>.A<N2 2> does not have a type.

FATAL: Atom .R<bmi 102>.A<N3 3> does not have a type.

FATAL: Atom .R<bmi 102>.A<C4 4> does not have a type.

FATAL: Atom .R<bmi 102>.A<C5 5> does not have a type.

FATAL: Atom .R<bmi 102>.A<C6 6> does not have a type.

FATAL: Atom .R<bmi 102>.A<C7 7> does not have a type.

FATAL: Atom .R<bmi 102>.A<C8 8> does not have a type.

FATAL: Atom .R<bmi 102>.A<C9 9> does not have a type.

FATAL: Atom .R<bmi 102>.A<C10 10> does not have a type.

FATAL: Atom .R<bmi 102>.A<H11 11> does not have a type.

FATAL: Atom .R<bmi 102>.A<H12 12> does not have a type.

FATAL: Atom .R<bmi 102>.A<H13 13> does not have a type.

FATAL: Atom .R<bmi 102>.A<H14 14> does not have a type.

FATAL: Atom .R<bmi 102>.A<H15 15> does not have a type.

FATAL: Atom .R<bmi 102>.A<H16 16> does not have a type.

FATAL: Atom .R<bmi 102>.A<H17 17> does not have a type.

FATAL: Atom .R<bmi 102>.A<H18 18> does not have a type.

FATAL: Atom .R<bmi 102>.A<H19 19> does not have a type.

FATAL: Atom .R<bmi 102>.A<H20 20> does not have a type.

FATAL: Atom .R<bmi 102>.A<H21 21> does not have a type.

FATAL: Atom .R<bmi 102>.A<H22 22> does not have a type.

FATAL: Atom .R<bmi 102>.A<H23 23> does not have a type.

FATAL: Atom .R<bmi 102>.A<H24 24> does not have a type.

FATAL: Atom .R<bmi 102>.A<H25 25> does not have a type.

Failed to generate parameters

Parameter file was not saved.

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Dec 02 2013 - 08:30:02 PST

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