Thursday, August 26, 2004
Using AMBER for Molecular Dynamics
I have a peptide tail that has a CYS residue as the n-terminous and when I run tleap:
tleap -s -f leaprc.ff99.tf using what I thought was the correct pdb syntax file
...
.... etc
which has already been pre-processed using protonate I get the following error message.
Created a new atom named: HS within residue: .R
FATAL: Atom .R.A does not have a type
I have check the PDB file and it seems to have the correct number of hydrogens so why is it trying to add another? I have also look through the leap libraries and noticed a number of difference nomenclatures for the hydrogen on the sulfur (HS, HGS, HG) and have tried those permutations in the PDB file without success.
Well, I was about to send off my message to the amber@scripps.edu mirror site for help in the AMBER group and I finally discovered my error. The line in the library was
"HSG" "HS" 0 -1 0.0
Indicating that the correct nomenclature was HSG! Even though the standard PDB format would be HG and the AMBER type is HS. Anyway, I am glad to get over this small error. I was able to run a set of molecular dynamics calculations to test out sander (the main program in the AMBER suite) and a solution was computed. My next task is to streamline the whole process and run a set of 50 to 100 structures to ensure that they converge together.
I have a peptide tail that has a CYS residue as the n-terminous and when I run tleap:
tleap -s -f leaprc.ff99.tf using what I thought was the correct pdb syntax file
...
ATOM 1 N CYS 1 1.325 0.000 0.000
ATOM 2 H1 CYS 1 0.858 -0.893 0.114
ATOM 3 H2 CYS 1 1.960 0.150 0.776
ATOM 4 H3 CYS 1 0.635 0.742 -0.020
ATOM 5 CA CYS 1 2.073 0.000 -1.245
ATOM 6 HA CYS 1 1.393 -0.209 -2.045
ATOM 7 CB CYS 1 2.727 1.357 -1.513
ATOM 8 3HB CYS 1 3.751 1.327 -1.194
ATOM 9 2HB CYS 1 2.204 2.118 -0.965
ATOM 10 SG CYS 1 2.660 1.743 -3.300
ATOM 11 HG CYS 1 3.231 2.924 -3.520
ATOM 12 C CYS 1 3.105 -1.128 -1.186
ATOM 13 O CYS 1 3.825 -1.264 -0.198
ATOM 14 N ARG 2 3.143 -1.909 -2.256
ATOM 15 H ARG 2 2.515 -1.728 -3.026
.... etc
which has already been pre-processed using protonate I get the following error message.
Created a new atom named: HS within residue: .R
FATAL: Atom .R
I have check the PDB file and it seems to have the correct number of hydrogens so why is it trying to add another? I have also look through the leap libraries and noticed a number of difference nomenclatures for the hydrogen on the sulfur (HS, HGS, HG) and have tried those permutations in the PDB file without success.
Well, I was about to send off my message to the amber@scripps.edu mirror site for help in the AMBER group and I finally discovered my error. The line in the library was
"HSG" "HS" 0 -1 0.0
Indicating that the correct nomenclature was HSG! Even though the standard PDB format would be HG and the AMBER type is HS. Anyway, I am glad to get over this small error. I was able to run a set of molecular dynamics calculations to test out sander (the main program in the AMBER suite) and a solution was computed. My next task is to streamline the whole process and run a set of 50 to 100 structures to ensure that they converge together.
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