You need to set ntr=1 to turn on restraints. 500 is pretty strong.
Where did the rest of the parameters come from - gaff?
You might try just a single bicarbonate to simplify things.
On Wed, Jul 20, 2022, 5:30 PM Christian Seitz <cseitz.ucsd.edu> wrote:
> Hi Carlos,
>
> I did a geometry optimization and then resp calculation to get the
> bicarbonate parameters, and created a .lib file for tleap. I can provide
> further details as necessary. Here is my full minimization input file:
>
> Minimize
> &cntrl
> imin=1,
> ntx=1,
> irest=0,
> maxcyc=10000,
> ncyc=5000,
> ntpr=10,
> ntwx=0,
> cut=8.0,
> restraint_wt=500.0,
> restraintmask=':MOL'
> /
>
> Best,
> Christian
>
> On Wed, Jul 20, 2022 at 2:03 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> Your restraint energy is 0,so I think your setup isn't right. What's your
>> full input file?
>> Also where did you get the bicarbonate parameters? The 1-4 eel is
>> unprintably high, so I suspect some intramolecular interaction is off.
>>
>>
>> On Wed, Jul 20, 2022, 4:53 PM Christian Seitz via AMBER <
>> amber.ambermd.org> wrote:
>>
>>> Hello,
>>>
>>> I added some bicarbonate ions to my protein of interest through packmol,
>>> and have been trying to minimize it. Whether I add counterions, water, or
>>> neither, I keep getting the same type of errors. The minimization will
>>> start, and shortly afterwards the energy of the bicarbonate ions will get
>>> very high until the system crashes with a segmentation fault:
>>>
>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>> 180 -2.9907E+07 9.3976E+10 9.8870E+12 O2 6302
>>>
>>> BOND = 695.1052 ANGLE = 5340.6089 DIHED =
>>> 5674.3885
>>> VDWAALS = -2632.3300 EEL = -26695.4667 HBOND =
>>> 0.0000
>>> 1-4 VDW = 1293.9465 1-4 EEL = ************* RESTRAINT =
>>> 0.0000
>>>
>>> This happens even though I am restraining the bicarbonate ions in my
>>> minimization:
>>>
>>> restraintmask=':MOL'
>>>
>>> and looking at the structure, the bicarbonate ions of very high energy
>>> are
>>> not particularly close to anything else. I thought these high energies
>>> would come with overlapping atoms, but this doesn't appear to be the
>>> case.
>>> What else can I try? Thanks in advance!
>>>
>>> Best,
>>> Christian
>>> --
>>> *Christian Seitz*
>>> PhD Candidate, Biochemistry & Biophysics | UC-San Diego
>>> NSF GRFP Fellow, Amgen Scholar
>>> McCammon lab <https://mccammon.ucsd.edu/> and Amaro lab
>>> <https://amarolab.ucsd.edu/>
>>> cseitz.ucsd.edu <cseitz.elon.edu>
>>> [image: www.linkedin.com/in/christianseitz21
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>>> ]
>>>
>>> <http://www.linkedin.com/in/christianseitz21
>>> <https://urldefense.com/v3/__http://www.linkedin.com/in/christianseitz21__;!!Mih3wA!DmrVtFvyc76M0nsVwq26b9RraJOm8w6ERPIN8ErZrqFUAOGAv3Q8z9y9o5Bbi1cy4e2D9FyAhewEVRk8EMGy0XYUjw$>
>>> >
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>>>
>>
>
> --
> *Christian Seitz*
> PhD Candidate, Biochemistry & Biophysics | UC-San Diego
> NSF GRFP Fellow, Amgen Scholar
> McCammon lab <https://mccammon.ucsd.edu/> and Amaro lab
> <https://amarolab.ucsd.edu/>
> cseitz.ucsd.edu <cseitz.elon.edu>
> [image: www.linkedin.com/in/christianseitz21]
>
> <http://www.linkedin.com/in/christianseitz21>
>
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Received on Thu Aug 04 2022 - 13:35:13 PDT
