AMBER Archive (2005)

Subject: AMBER: details of new aminoacid

From: Gustavo Pierdominici Sottile (gsottile_at_unq.edu.ar)
Date: Tue Jan 18 2005 - 07:01:15 CST

Hi, I send the details of the problems with the developing of a new
aminoacid. Suppose I have to designate a new amino acid. I create the
archive .in that looks like this (it is not complete)
  0 0 2
POCOIMAGIN
trp1.db4
 AVO INT 1
 CORR OMIT DU BEG
   0.00000
   1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
   2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
   3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
   4 N N M 3 2 1 1.335 116.600 180.000 -0.41570
   5 H H E 4 3 2 1.020 119.800 0.000 0.27190
   6 CA CT M 4 3 2 1.470 121.900 180.000 -0.05270
   7 HA H1 E 6 4 3 1.090 107.300 300.000 0.08660
   8 CB CT 3 6 4 3 1.550 110.500 60.000 0.03550
   9 HB2 HC E 8 6 4 1.090 108.400 173.900 0.05730
  10 HB3 HC E 8 6 4 1.090 109.800 57.500 0.05730
  11 CG C* S 8 6 4 1.510 112.600 292.400 -0.09950
  12 CD1 CW B 11 8 6 1.370 129.100 126.700 -0.05060
  13 NE1 NA B 12 11 8 1.390 107.100 190.000 -0.31550
  14 HE1 H E 13 12 11 1.020 121.700 167.400 0.31710
  15 CE2 CN S 13 12 11 1.380 113.200 350.600 0.07850
  16 CZ2 CA B 15 13 12 1.400 133.900 183.700 -0.15890

Then I execute the command tleap:
tleap -f leaprc.ff94
Once it is executed I write
loadamberprep "filename" (the name of the file which part is shown above)
mad= loadpdb "name of the pdb file"
when I write saveamberparm mad top.l crd.l, the following lines appears

Could not find bond parameter for: CW - C
Could not find angle parameter: C* - CW - C

The problem is that there are no atoms of this type joined in the new
aminoacid. I do not have two atoms of type CW and C joined. The same happens
with angles and dihedral.
It also appears one warning for each water molecule. All of then states the
same:

WARNING: There is a bond of 3.464102 angstroms between:
------- .R<WAT 7341>.A<H2 2> and .R<WAT 7341>.A<O 3>

This is not true because all the bonds in water molecule are smaller then 1
angstroms.

Thanks in advance
Gustavo

   

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