Dear Prabir,
You could use REDServer Development .:
https://upjv.q4md-forcefieldtools.org/REDServer-Development/
See tutorial .:
https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#SpltV
https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#IV1
https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#V2
https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo5.pdf
I hope this helps
Best Francois
> As I mentioned in my earlier email that I am going to follow the procedure
> suggested by Carlos to preserve OL15 description as much as possible. I am
> still seeking a suggestion regarding the charge parameterization. To get
> the charge parameters, I am doing an optimization using gaussian 16 with
> B3LYP/6-31G* followed by RESP charge calculation at HF/6-31G* level. The
> charge distribution that I got is significantly different from the
> unprotonated cytosine of the original OL15 parameter for all the atoms
> including sugar and phosphate. Please note that I am doing the optimization
> and the RESP charge calculation on the entire protonated cytosine including
> sugar ring and phosphate. While such charge redistribution is expected due
> to the protonation of cytosine N3, I am wondering if a better approach
> might be to optimize and calculate the charge of the base alone, so that
> there is no need to change the charge distribution in the sugar or
> phosphate. This would help in obtaining the new charge distribution,
> preserving the OL15 description to the maximum extent. Please comment on
> this.
>
> I appreciate any help/suggestion.
>
>
> On Thu, Aug 8, 2024 at 8:59 AM Prabir Khatua <pkhatua.gitam.edu> wrote:
>
>> Thanks Carlos for the reply! Loading the frcmod file before the mol2 file
>> worked for me.
>>
>> In fact, I wanted to follow the complex procedure you mentioned that is
>> taking OL15 force field parameters as much as possible and then using the
>> gaff generated parameter for the added part.
>>
>> Thanks once again for the suggestion and help!
>> Prabir
>>
>> On Wed, 7 Aug 2024 at 7:13 PM Carlos Simmerling <
>> carlos.simmerling.gmail.com> wrote:
>>
>>> 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.
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Received on Thu Aug 08 2024 - 07:30:02 PDT
