others here may have more detailed info for you, but the frcmod file you
shared does indeed have the o-p3-os params, you might want to try loading
those parameters before you load the mol2, not after.
also the log file gets appended every time you run it, so it can be more
helpful if you remove the log file before re-running leap so that it
contains only the most recent attempt. otherwise it contains the history of
previous errors even if they were fixed later and it is more difficult to
follow.
some other suggestions: loading multiple leaprc files can get confusing.
for example, loading both gaff and gaff2 should not be needed, you should
choose 1 and use that. also it looks like you have no standard DNA here so
loading the OL15 learprc is not needed.
finally, keep in mind that using gaff/gaff2 for your DNA will mean that the
entire monomer is described by gaff, and it will not have any of the
DNA-specific adjustments applied to that monomer (backbone dihedrals, sugar
puckers and so on). This means it may behave differently from standard
cytosine just because of the parameter differences and not only because of
the protonation change. To be more clear, a standard cytosine using gaff
and using OL15 will not necessarily behave the same, so you need to be
careful in how you interpret the results of the protonation. A better (but
more complex) approach would be to use the OL15 parameters as much as
possible, and then use gaff only for the part of the monomer that differs
from the standard base. This would preserve the OL15 description as much as
possible. This does require some force field expertise, and you may get
more specific advice from experts here in DNA force fields.
On Wed, Aug 7, 2024 at 3:26 AM Prabir Khatua via AMBER <amber.ambermd.org>
wrote:
> Dear Amber users,
>
> I am getting the following error while trying to generate the force field
> for a protonated cytosine (not as 5' or 3' or neutral one) using the OL15
> force field in Amber 24.
>
> /apps/scratch/compile/amber24/bin/teLeap: Error!
> Could not find angle parameter for atom types: o - p3 - os
> for atom O1 at position -3.028000, -2.260000, 1.553000,
> atom P1 at position -2.521000, -1.721000, 0.281000,
> and atom O3 at position -3.395000, -0.527000, -0.304000.
>
> /apps/scratch/compile/amber24/bin/teLeap: Error!
> Could not find angle parameter for atom types: o - p3 - os
> for atom O2 at position -1.455000, -2.224000, -0.617000,
> atom P1 at position -2.521000, -1.721000, 0.281000,
> and atom O3 at position -3.395000, -0.527000, -0.304000.
>
> It seems like it's unable to find the above mentioned parameter. However, I
> do not know which force field I should source. For your information, I am
> attaching the entire log file, input leap file, mol2, and frcmod files if
> needed. Please help me to fix this issue.
>
> Thanks in advance!
> Prabir
>
> *----------------------------------------*
>
> *Prabir Khatua, PhD*
>
> *Assistant Professor, Department of Chemistry*
>
> *GITAM School of Science *
> *GITAM (Deemed to be University)*
> *Bengaluru-562163**, India*
>
>
> *Website: https://prabir07chem.wixsite.com/computational-biophy
> <https://prabir07chem.wixsite.com/computational-biophy>*
> --------------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 07 2024 - 07:00:02 PDT
