2
$\begingroup$

I am trying to parameterize a novel molecule which has atoms not included gaff or parm force field. I finished parameterizing vdw-bond and angle force field. Also I did PES Scan for dihedrals and I wrote them in a frcmod file as truncated fourrier integral. Yes, actually most probably I will not need paramfit parameterization but I wondered and I tested paramfit.

Here is tutorial: http://ambermd.org/tutorials/advanced/tutorial23/index.html#Introduction

I succesfully finished this tutorial and after this I tried to apply paramfit to my "monomer" and "not included any force field" molecule. But xleap gives some error message and I locked completely. I changed gen_conformers.sh (Don't click if you don't want to download!) for my molecule and I couldn't obtain different conformations.

Then I tested where was the mistake. I created leapin file like this:

source oldff/leaprc.ff99
addAtomTypes { { "B" "B" "sp3" } }
addAtomTypes { { "O" "O" "sp3" } }
addAtomTypes { { "C" "C" "sp3" } }
a=loadmol2 bor.mol2
loadamberparams bor.dat
impose a {1 1}, { {"H1" "O2" "B3" "O4" 72.000} }
impose a {1 1}, { {"O12" "B3" "O4" "C5" 19.000} }
impose a {1 1}, { {"B3" "O4" "C5" "C6" 108.000} }
impose a {1 1}, { {"B3" "O12" "C13" "H18" 11.000} }
saveamberparm a a_1.prmtop a_1.mdcrd
check a
quit

then I run this file with this command:

xleap -f leapin

but after that leap.log file:

  Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for  C-H-C-H
        atoms are: C2 H5 C1 H6
 ** Warning: No sp2 improper torsion term for  C-H-C-H
        atoms are: C1 H2 C2 H3
 ** Warning: No sp2 improper torsion term for  C-H-C-H
        atoms are: C1 H2 C2 H4
 ** Warning: No sp2 improper torsion term for  C-H-C-H
        atoms are: C1 H3 C2 H4
 ** Warning: No sp2 improper torsion term for  H-H-C-H
        atoms are: H2 H3 C2 H4
 ** Warning: No sp2 improper torsion term for  C-H-C-H
        atoms are: C4 H10 C3 H11
 ** Warning: No sp2 improper torsion term for  C-H-C-H
        atoms are: C3 H7 C4 H8
 ** Warning: No sp2 improper torsion term for  C-H-C-H
        atoms are: C3 H7 C4 H9
 ** Warning: No sp2 improper torsion term for  C-H-C-H
        atoms are: C3 H8 C4 H9
 ** Warning: No sp2 improper torsion term for  H-H-C-H
        atoms are: H7 H8 C4 H9
 total 7 improper torsions applied

and after that, even if I changed angles many many times in "impose" command

 impose a {1 1}, { {"B3" "O4" "C5" "C6" 108.000} }

I obtained the same *.inpcrd files and I couldn't generate different conformation gaussian job file. So how can I apply paramfit for a ligand? (or monomer)

$\endgroup$

closed as unclear what you're asking by Karl, Mithoron, Todd Minehardt, Jon Custer, tschoppi Feb 19 at 9:08

Please clarify your specific problem or add additional details to highlight exactly what you need. As it's currently written, it’s hard to tell exactly what you're asking. See the How to Ask page for help clarifying this question. If this question can be reworded to fit the rules in the help center, please edit the question.

  • 3
    $\begingroup$ amber has a mailing list, you may have better luck on that. lists.ambermd.org/mailman/listinfo/amber $\endgroup$ – Charlie Crown Feb 17 at 20:16
  • 1
    $\begingroup$ What is "monomer or ligand" ? We're not a helpdesk here, questions should make sense to other people, too. $\endgroup$ – Karl Feb 17 at 21:50
  • 1
    $\begingroup$ I'm voting to close this question as off-topic because it's a question about how to use AMBER. $\endgroup$ – Todd Minehardt Feb 18 at 18:09
  • $\begingroup$ I think opposite. The question is about applying genetic algorithm (G.A) to dihedrals. And paramfit is the only software can do this.( Why I am saying this? here: doi.org/10.1002/jcc.23775 ) So even if user don't want to talk about paramfit he/she has to talk about paramfit. Another problem that the user faces is not to be able to save the related coordinate files by turning the dihedral angles.(xleap) Charmm, tinder, gromacs softwares are already using "amber ff " so in this respect, all molecular simulations have to do with "amber" thus problem is more complex than it looks. $\endgroup$ – Baris Vvolf Feb 19 at 8:36
  • 3
    $\begingroup$ Erdem, I think I found answer, ( Iwas facing with the same problem for about 1 month) I tested for my molecule and I got true results: to obtain rand conformers; Instead of xleap use another program and skip this step of the paramfit tutorial with these conformers (you will need to change *.dat files according to your dihedral angels, this is fatal important). You can use this program: en.freedownloadmanager.org/Windows-PC/ArgusLab-FREE.html Good Luck! $\endgroup$ – Baris Vvolf Feb 19 at 10:00