It can be helpful also to make sure to use the full double precision cuda
version (dpdp). But in many cases the cpu version or even sander are needed
for difficult initial structures.
On Mon, Sep 16, 2024, 6:53 PM Martin Juhás <juhasm.faf.cuni.cz> wrote:
> Hi,
>
> Did you try sander and pmemd, pmemd.cuda?
>
> I had similar problems with bond "stretching" despite everything looked
> normal in frcmod etc.. It was so bad that the mdgx was unable to generate
> inputs for torsion calculations because the structures were distorted
> during minimization step. I was unable to find a root cause
> unfortunately. However, I noticed the issues were occuring only when
> minimizing using pmemd, when I tried sander it was OK. Then pmemd.cuda was
> also OK, if starting from sander minimized structure.
>
> In my case the structures were boron clusters with a net charge. Maybe
> pmemd and sander calculate things differently and thus have effects,
> undesired, on some specific bonds?
>
> Hope this helps...
>
> MJ
>
> Odoslané z aplikácie Outlook pre Android <https://aka.ms/AAb9ysg>
> ------------------------------
> *From:* Maciej Spiegel via AMBER <amber.ambermd.org>
> *Sent:* Monday, September 16, 2024 10:32:33 PM
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Cc:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Subject:* Re: [AMBER] Issue with Bonds after Ligand Parameterization for
> MD Simulation
>
> [EXTERNAL EMAIL]
>
>
> I have noticed some weird behaviour. On my HPC there’s amber16 and
> amber22. I did use the latter. Regardless, I use „-at gaff2”, „-at gaff” or
> „-at amber”, at the stage of "antechamber -i LIG_resp.ac -fi ac -c wc -cf
> LIG.crg” command, the following error emerges:
>
> ************
> Welcome to antechamber 22.0: molecular input file processor.
>
> Info: acdoctor mode is on: check and diagnose problems in the input file.
> Info: The atom type is set to gaff; the options available to the -at flag
> are
> gaff, gaff2, amber, bcc, and sybyl.
>
> -- Check Format for ac File --
> Status: pass
> -- Check Unusual Elements --
> Status: pass
> -- Check Open Valences --
> Status: pass
> -- Check Geometry --
> for those bonded
> for those not bonded
> Status: pass
> -- Check Weird Bonds --
> /opt/exp_soft/local/skylake/amber/22/bin/wrapped_progs/antechamber: Fatal
> Error!
> Weird atomic valence (0) for atom (ID: 1, Name: O1).
> Possible open valence.
> ************
>
> However, when using amber/16, all I got is:
>
> ************
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase PSCUTOFF in define.h and recompile bondtype.c
> Be cautious, use a large value of PSCUTOFF (>100) will significantly
> increase the computation time
> Unknown output file format:
> ************
>
> Weird behaviour or intentional prevention in the newer version?
>
> –
> Maciej Spiegel, MPharm PhD
> assistant professor
> .GitHub <https://farmaceut.github.io/>
>
> Department of Organic Chemistry and Pharmaceutical Technology,
> Faculty of Pharmacy, Wroclaw Medical University
> Borowska 211A, 50-556 Wroclaw, Poland
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g>
>
> > Wiadomość napisana przez Carlos Simmerling <carlos.simmerling.gmail.com>
> w dniu 16.09.2024, o godz. 22:09:
> >
> > you might try using parmed to check the parameters that are present in
> the prmtop file itself, in case something went wrong in building the system.
> >
> > On Mon, Sep 16, 2024 at 3:50 PM Maciej Spiegel <
> maciej.spiegel.umw.edu.pl <mailto:maciej.spiegel.umw.edu.pl
> <maciej.spiegel.umw.edu.pl>>> wrote:
> >> Something seems to be more than just wrong: in the frcmod file, there
> is:
> >>
> >>>> ca-os 357.50 1.370
> >>>> c2-os 371.30 1.360
> >> but , after MD, these values are 1.771 Å and 1.790 Å. Next, in the file
> there is:
> >>
> >>>> c2-ca 398.40 1.385
> >>
> >> but it becomes 1.782A. And similarly,
> >>
> >>>> c2-c2 481.80 1.334
> >>
> >> elongated to 1.689A.
> >>
> >> The reference image (https://i.sstatic.net/YF0S4qmx.png)
> >>
> >> –
> >> Maciej Spiegel, MPharm PhD
> >> assistant professor
> >> .GitHub <https://farmaceut.github.io/>
> >>
> >> Department of Organic Chemistry and Pharmaceutical Technology,
> >> Faculty of Pharmacy, Wroclaw Medical University
> >> Borowska 211A, 50-556 Wroclaw, Poland
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g>
> >>
> >>> Wiadomość napisana przez Carlos Simmerling <
> carlos.simmerling.gmail.com <mailto:carlos.simmerling.gmail.com
> <carlos.simmerling.gmail.com>>> w dniu 16.09.2024, o godz. 21:02:
> >>>
> >>> use the numbers from the "BOND" section, along with measurements of
> the bond lengths from the structure that concerns you.
> >>>
> >>> On Mon, Sep 16, 2024 at 3:01 PM Maciej Spiegel <
> maciej.spiegel.umw.edu.pl <mailto:maciej.spiegel.umw.edu.pl
> <maciej.spiegel.umw.edu.pl>>> wrote:
> >>>> The generated .frcmod is as follows:
> >>>>
> >>>> ******************
> >>>> Remark line goes here
> >>>> MASS
> >>>> os 16.000 0.465
> >>>> ca 12.010 0.360
> >>>> c2 12.010 0.360
> >>>> o 16.000 0.434
> >>>> oh 16.000 0.465
> >>>> ho 1.008 0.135
> >>>> ha 1.008 0.135
> >>>>
> >>>> BOND
> >>>> ca-os 357.50 1.370
> >>>> c2-os 371.30 1.360
> >>>> ca-ca 378.60 1.398
> >>>> c2-ca 398.40 1.385
> >>>> c2-o 635.20 1.225
> >>>> c2-c2 481.80 1.334
> >>>> c2-oh 402.30 1.339
> >>>> ho-oh 563.50 0.973
> >>>> ca-ha 395.70 1.086
> >>>> ca-o 606.50 1.236
> >>>> ca-oh 365.60 1.364
> >>>>
> >>>> ANGLE
> >>>> ca-ca-os 87.300 119.200
> >>>> c2-c2-os 88.700 121.870
> >>>> ca-c2-os 88.000 122.800 same as ce-c2-os, penalty score= 2.2
> >>>> c2-os-ca 67.800 118.200
> >>>> c2-ca-ca 68.900 120.600
> >>>> ca-ca-ca 68.800 120.020
> >>>> ca-ca-ha 48.700 119.880
> >>>> ca-c2-o 91.400 123.590 same as cc-c2-o , penalty score= 2.0
> >>>> c2-c2-ca 71.600 117.000
> >>>> c2-c2-oh 89.300 122.170
> >>>> c2-c2-c2 71.500 121.810
> >>>> c2-c2-o 89.800 130.890
> >>>> c2-oh-ho 51.800 107.630
> >>>> ca-ca-o 89.500 123.260
> >>>> ca-ca-oh 87.200 119.900
> >>>> ca-oh-ho 50.700 108.580
> >>>>
> >>>> DIHE
> >>>> c2-ca-ca-os 4 14.500 180.000 2.000
> >>>> ca-ca-ca-os 4 14.500 180.000 2.000
> >>>> ha-ca-ca-os 4 14.500 180.000 2.000
> >>>> os-c2-ca-ca 4 2.800 180.000 2.000
> >>>> c2-c2-os-ca 2 2.100 180.000 2.000
> >>>> ca-c2-os-ca 2 2.100 180.000 2.000
> >>>> o -c2-ca-ca 4 2.800 180.000 2.000
> >>>> c2-c2-ca-ca 4 2.800 180.000 2.000
> >>>> ca-ca-ca-ca 4 14.500 180.000 2.000
> >>>> ca-ca-ca-ha 4 14.500 180.000 2.000
> >>>> ca-c2-c2-oh 4 26.600 180.000 2.000
> >>>> c2-c2-c2-ca 4 26.600 180.000 2.000
> >>>> c2-ca-ca-ca 4 14.500 180.000 2.000
> >>>> c2-ca-ca-ha 4 14.500 180.000 2.000
> >>>> c2-c2-oh-ho 1 1.120 180.000 2.000
> >>>> c2-c2-c2-os 4 26.600 180.000 2.000
> >>>> o -c2-c2-oh 4 26.600 180.000 2.000
> >>>> c2-c2-c2-o 4 26.600 180.000 2.000
> >>>> oh-c2-c2-os 4 26.600 180.000 2.000
> >>>> ca-ca-ca-o 4 14.500 180.000 2.000
> >>>> ha-ca-ca-o 4 14.500 180.000 2.000
> >>>> ha-ca-ca-ha 4 14.500 180.000 2.000
> >>>> ca-ca-os-c2 2 1.800 180.000 2.000
> >>>> ca-ca-ca-oh 4 14.500 180.000 2.000
> >>>> ca-ca-oh-ho 1 0.835 180.000 2.000
> >>>> ha-ca-ca-oh 4 14.500 180.000 2.000
> >>>> o -ca-ca-oh 4 14.500 180.000 2.000
> >>>>
> >>>> IMPROPER
> >>>> ca-ca-ca-os 1.1 180.0 2.0 Using the
> default value
> >>>> c2-ca-ca-ca 1.1 180.0 2.0
> >>>> c2-ca-c2-o 1.1 180.0 2.0 Using the
> default value
> >>>> c2-c2-c2-oh 1.1 180.0 2.0 Using the
> default value
> >>>> ca-ca-ca-ha 1.1 180.0 2.0 Using
> general improper torsional angle X- X-ca-ha, penalty score= 6.0)
> >>>> ca-ca-ca-o 1.1 180.0 2.0 Using the
> default value
> >>>> c2-ca-c2-os 1.1 180.0 2.0 Using the
> default value
> >>>> ca-ca-ca-oh 1.1 180.0 2.0 Using the
> default value
> >>>>
> >>>> NONBON
> >>>> os 1.7713 0.0726
> >>>> ca 1.8606 0.0988
> >>>> c2 1.8606 0.0988
> >>>> o 1.7107 0.1463
> >>>> oh 1.8200 0.0930
> >>>> ho 0.3019 0.0047
> >>>> ha 1.4735 0.0161
> >>>> ******************
> >>>>
> >>>>
> >>>> –
> >>>> Maciej Spiegel, MPharm PhD
> >>>> assistant professor
> >>>> .GitHub <https://farmaceut.github.io/>
> >>>>
> >>>> Department of Organic Chemistry and Pharmaceutical Technology,
> >>>> Faculty of Pharmacy, Wroclaw Medical University
> >>>> Borowska 211A, 50-556 Wroclaw, Poland
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g>
> >>>>
> >>>>> Wiadomość napisana przez Carlos Simmerling <
> carlos.simmerling.gmail.com <mailto:carlos.simmerling.gmail.com
> <carlos.simmerling.gmail.com>>> w dniu 16.09.2024, o godz. 20:49:
> >>>>>
> >>>>> it's hard to tell from a picture, you might want to measure the bond
> lengths and compare to those in the frcmod file.
> >>>>>
> >>>>> On Mon, Sep 16, 2024 at 2:35 PM Maciej Spiegel via AMBER <
> amber.ambermd.org <mailto:amber.ambermd.org <amber.ambermd.org>>> wrote:
> >>>>>> Hello,
> >>>>>>
> >>>>>> I found a tutorial and followed it to parametrise the ligand below:
> >>>>>>
> >>>>>> https://i.sstatic.net/6HyFgwEB.png
> >>>>>>
> >>>>>> To say, the following commands were utilised consecutively:
> >>>>>>
> >>>>>> ************
> >>>>>> antechamber -i LIG.mol2 -fi mol2 -o LIG.gjf -fo gcrt -gv 1 -ge
> LIG.gesp -pf y -nc -2 -at gaff2
> >>>>>> g16 LIG.gjf
> >>>>>> antechamber -i LIG.gesp -fi gesp -o LIG_resp.ac -fo ac -c resp -at
> gaff2 -rn LIG -pf y
> >>>>>> antechamber -i LIG_resp.ac -fi ac -c wc -cf LIG.crg
> >>>>>> espgen -i LIG.gesp -o LIG.esp
> >>>>>> respgen -i LIG_resp.ac -o LIG.respin1 -f resp1
> >>>>>> respgen -i LIG_resp.ac -o LIG.respin2 -f resp2
> >>>>>> resp -O -i LIG.respin1 -o LIG.respout1 -p LIG.pch1 -q LIG_mod.crg
> -t LIG.chg1 -e LIG.esp
> >>>>>> resp -O -i LIG.respin2 -o LIG.respout2 -p LIG.pch2 -q LIG.chg1 -t
> LIG.chg2 -e LIG.esp
> >>>>>> cp LIG_resp.ac LIG_resp_final.ac
> >>>>>> prepgen -i LIG_resp_final.ac -o LIG.prepc -f car -rn LIG
> >>>>>> parmchk2 -i LIG.prepc -o LIG.frcmod -f prepc -p
> $AMBERHOME/dat/leap/parm/gaff2.dat -pf 1 -a Y
> >>>>>> ************
> >>>>>>
> >>>>>> Then using tLeap:
> >>>>>>
> >>>>>> ************
> >>>>>> source leaprc.gaff2
> >>>>>> source leaprc.protein.ff19SB
> >>>>>> source leaprc.water.tip3p
> >>>>>> source leaprc.lipid21
> >>>>>> loadamberparams frcmod.ionsjc_tip3p
> >>>>>> loadamberprep LIG.prepc
> >>>>>> loadamberparams LIG.frcmod
> >>>>>> prot = loadpdb MD.pdb
> >>>>>> charge prot
> >>>>>> addions2 prot Cl- 3
> >>>>>> solvateoct prot TIP3PBOX 12.0
> >>>>>> saveamberparm prot MD.prmtop MD.inpcrd
> >>>>>> ************
> >>>>>>
> >>>>>> Everything went fine. However, once the molecular dynamics started,
> I noticed that the bonds appear *off*, e.g., the C-O-C bonds seem elongated.
> >>>>>>
> >>>>>> https://i.sstatic.net/FGLRu3Vo.png
> >>>>>>
> >>>>>> I am not very keen with MD and henceforth don't know where might be
> the issue. The `atomtypes` seem reasonable:
> >>>>>>
> >>>>>> https://i.sstatic.net/vfRt5Co7.png
> >>>>>>
> >>>>>> Thanks in advance!
> >>>>>> –
> >>>>>> Maciej Spiegel, MPharm PhD
> >>>>>> assistant professor
> >>>>>> .GitHub <https://farmaceut.github.io/>
> >>>>>>
> >>>>>> Department of Organic Chemistry and Pharmaceutical Technology,
> >>>>>> Faculty of Pharmacy, Wroclaw Medical University
> >>>>>> Borowska 211A, 50-556 Wroclaw, Poland
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org <mailto:AMBER.ambermd.org <AMBER.ambermd.org>>
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>
>
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Received on Mon Sep 16 2024 - 16:30:02 PDT
