Hi,
I am a beginner in using AMBER. I have been trying to create some input
files for a DNA sequence that contains 5-methyl-cytosine. I have an input
PDB file that contains DNA complexed with an enzyme, however I am just
interested in the conformation of the DNA molecule. Can you please check if
I am following the right steps?
1. Delete everything from the PDB that is not related to the DNA
sequence.
2. pdb4amber -i orig.pdb -o new.pdb --reduce –dry (copied from Amber
manual). On running this I obtained, The following non-standard residue
names in the original PDB file are not recognized by Amber and have been
written to the separate file dnaReducedDry_nonprot.pdb 5CM
3. How do we choose the force field? parmbsc1 or OL15? Can we use
both? I found the library and frcmod files for parmbsc1 (
https://mmb.irbbarcelona.org/ParmBSC1/help.php?id=download), OL15 (OL Force
Field Refinement for RNA and DNA Simulations (upol.cz)
<
https://fch.upol.cz/ff_ol/downloads.php>) but I am not able to use either
of these. My leap.in file currently looks like the following,
# source leaprc.ff14SB
# addAtomTypes {
# { "C1" "C" "sp2" }
# { "C2" "C" "sp2" }
# { "CI" "C" "sp3" }
# { "CE" "C" "sp3" }
# }
# loadoff parmBSC1.lib
# loadamberparams parmBSC1.frcmod
source leaprc.ff14SB
addAtomTypes {
{ "C7" "C" "sp3" }
{ "CJ" "C" "sp3" }
{ "C1" "C" "sp2" }
{ "C2" "C" "sp2" }
}
loadoff ff-nucleic-OL15.lib
loadamberparams ff-nucleic-OL15.frcmod
parmMC = loadAmberParms frcmod.dat
saveOff parmMC parmMC.lib
loadAmberPrep dmc.in
loadOff parmMC.lib
dna1 = loadPdb dnaReducedDry.pdb
saveamberparm dna1 coords.prmtop coords.inpcrd
quit
When I am trying to use parmbsc1, I am getting the following error: Loading
parameters: ./parmBSC1.frcmod
Reading force field modification type file (frcmod)
Reading title:
Parmbsc1 force-field for DNA
ERROR: syntax error
!FATAL ERROR----------------------------------------
!FATAL: In file [list.c], line 437
!FATAL: Message: llListLoop called with NULL list
!
!ABORTING.
And when I am trying to use OL15, I am getting the following error:
Loading parameters: ./ff-nucleic-OL15.frcmod
Reading force field modification type file (frcmod)
Reading title:
OL15 force field for DNA (99bsc0-betaOL1-eps-zetaOL1-chiOL4) see
http://ffol.upol.cz
ERROR: syntax error
!FATAL ERROR----------------------------------------
!FATAL: In file [list.c], line 437
!FATAL: Message: llListLoop called with NULL list
!
!ABORTING.
4. Can you please suggest how I should proceed?
5.
http://archive.ambermd.org/201910/0005.html. Can I use these
parameters with the above force fields? But it is meant specifically for
the parmbsc0 force field.
6. In case the answer to the above question is yes (or if I was using
parmbsc0 force field), how do I load the parameter files in my input file
for tleap? How do I include the PREP and FRCMOD files? Is the following
sequence of commands correct? Also, what do the .dat and .in files
correspond to (is it FRCMOD and PREP file respectively)?
parmMC = loadAmberParams frcmod.dat
saveOff parmMC parmMC.lib
loadAmberPrep dmc.in
loadOff parmMC.lib
I will look forward to hearing from you.
Thanks and regards,
Nicy
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Received on Tue Jan 19 2021 - 14:30:02 PST
