Hello,
I have a PDB file of a protein-DNA complex bound to a silver ion. I am
trying to save topology and coordinate files for my simulations, but I run
into errors with the AG atom. I have looked in the forum and in the manuals
for help, and I believe I am doing everything correctly. The errors I get
are:
*/ihome/crc/build/amber/amber20_build-GNU/bin/teLeap: Error!Could not find
bond parameter for: O2 - Ag+Building angle
parameters./ihome/crc/build/amber/amber20_build-GNU/bin/teLeap: Error!Could
not find angle parameter: C - O2 - Ag+Building proper torsion
parameters./ihome/crc/build/amber/amber20_build-GNU/bin/teLeap: Error! **
No torsion terms for
O2-C-O2-Ag+/ihome/crc/build/amber/amber20_build-GNU/bin/teLeap: Error! **
No torsion terms for CX-C-O2-Ag+Building improper torsion
parameters. total 1273 improper torsions appliedBuilding H-Bond
parameters.Incorporating Non-Bonded
adjustments./ihome/crc/build/amber/amber20_build-GNU/bin/teLeap:
Warning!Parameter file was not saved.*
*This is the input file I am using for TLEAP:*
*i = createAtom AG Ag+ 1.0set i element "Ag"set i position { 0 0 0 }r =
createResidue AGadd r iAG = createUnit AGadd AG rsaveOff AG
./atomic_ions.libsource leaprc.protein.ff14SBsource leaprc.DNA.bsc1source
leaprc.water.tip3ploadoff atomic_ions.libmol=loadpdb
4wlw_corrected.pdbloadamberparams frcmod.ions1lm_126_tip3psolvateoct mol
TIP3PBOX 15.0addions mol Cl- 0addions mol Na+ 0addions mol Cl- 113addions
mol Na+ 113 check molsavepdb mol 4wlw_corr_solv.pdbsaveamberparm mol
4wlw_corr_solv.prmtop 4wlw_corr_solv.prmcrd*
I truly appreciate any and all suggestions! Thank you.
Alysia Mandato (University of Pittsburgh)
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Received on Mon Mar 07 2022 - 12:30:02 PST
