Dear AMBER users,
I have parametrizated a phosphonamide unit (MeP(O)(NHMe)2) in Amberv10
using Antechamber program and AM1-BCC charge method. A n3 atom type has
been assigned for the nitrogens linked to the P(O). I was changing the
nitrogen atom type to n (typical for amides) in the mol2 file and
creating the corresponding frcmod file. The prediction of the parameters
for the missing angles is OK and I had also and improper angle with a
constant 1.1 (c3-hn-n -p5).Then, I was using the inpcrd and prmtop files
created in xleap for relaxing this system (similar input file that in
tutorial B1 in polyAT_vac_init_min.in and modifications such as higher
cut, maxcyc = 1000, ncyc = 10). After that, the phosphorus lost the
tetrahedral geometry. In addition, the NHs do not have an appropriate
geometry. I was also changing the constant of the improper angle in the
frcmod file to higher values (until 10.5) and I had the same problems. I
have observed similar trend just keeping the nitrogens as n3. Any ideas
about what I am doing wrong?
I will appreciate very much any help and advice in this matter.
Thanks a lot in advance.
Gloria
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Received on Mon Jun 20 2011 - 11:00:04 PDT
