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From: (wrong string) Ã£o Sardinha <joao.sardinha.gmail.com>

Date: Thu, 8 Apr 2010 12:11:00 +0100

Dear Amber users

I'm trying to reproduce the angle force constants in GAFF as described

in J. Comput. Chem. 25: 1157-1174, (2004), in particular,

I'm using equations 5 and 6 to estimate missing angle force constants:

Kijk = 143.9 ZiCjZk (rij + rjk)-1 (èijk)-2 exp(-2D) (5)

D=(rij - rjk)2/(rij + rjk)2 (6)

for instance, for n4-c -o, gaff.dat has the following values:

Kijk = 69.6 èijk = 118.83

When I tried to use equations 5 and 6 to obtain Kijk:

Zi=1.212

Cj=1.339

Zk=1.219 (from table 4 in J. Comput. Chem. 25: 1157-1174, (2004))

rij=1.546 (from gaff.dat)

rjk=1.214 (from gaff.dat)

a completely different Kijk value was obtained: 23.3. This is a result

completely different from the result presented in gaff.dat : 69.6.

Is this a problem of unit convertion? I did not forget to use rad

instead of deg for the angle. Should I do anything else?

I tried to use the Kijk and rij to extract the constant C = ZiCjZk

for several identical atoms: for example c1-c -c1, c1-c1-c1 should

provide equal C values, instead values of 0.19 and 0.10 were obtained,

respectively.

Can anyone help me?

Thank you

Joao

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

Received on Thu Apr 08 2010 - 04:30:04 PDT

Date: Thu, 8 Apr 2010 12:11:00 +0100

Dear Amber users

I'm trying to reproduce the angle force constants in GAFF as described

in J. Comput. Chem. 25: 1157-1174, (2004), in particular,

I'm using equations 5 and 6 to estimate missing angle force constants:

Kijk = 143.9 ZiCjZk (rij + rjk)-1 (èijk)-2 exp(-2D) (5)

D=(rij - rjk)2/(rij + rjk)2 (6)

for instance, for n4-c -o, gaff.dat has the following values:

Kijk = 69.6 èijk = 118.83

When I tried to use equations 5 and 6 to obtain Kijk:

Zi=1.212

Cj=1.339

Zk=1.219 (from table 4 in J. Comput. Chem. 25: 1157-1174, (2004))

rij=1.546 (from gaff.dat)

rjk=1.214 (from gaff.dat)

a completely different Kijk value was obtained: 23.3. This is a result

completely different from the result presented in gaff.dat : 69.6.

Is this a problem of unit convertion? I did not forget to use rad

instead of deg for the angle. Should I do anything else?

I tried to use the Kijk and rij to extract the constant C = ZiCjZk

for several identical atoms: for example c1-c -c1, c1-c1-c1 should

provide equal C values, instead values of 0.19 and 0.10 were obtained,

respectively.

Can anyone help me?

Thank you

Joao

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Thu Apr 08 2010 - 04:30:04 PDT

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