[gmx-users] Equilibration Problem.

[Navneet Kumar Singh]

Hello Everyone!

Trying to simulate a system build in PACKMOL having peptides, water and
small molecules. Energy minimization and other process for setting up md
simulation went fine.

NVT AND NPT FOR 1000PS BUT system didn't Equilibrated.
Average required temperature maintained.





*Energy  Average   Err.Est. RMSD
Tot-Drift---Pressure
  0.261272 0.49  49.10611.55678  (bar)*


*Density213.361   0.58   1.18799
   4.08348 (kg/m^3)*


*Temperature   300.002   0.04  2.38265
-0.0854606  (K)*

*---*

*Temperature 300k is fine. But the density of the system is 213.361 and
attached graph (https://fil.email/ic2yZ4x3 )
shows unstable system. I extended it to 10 ns but still follows same
pattern. What can be the problem with this? Using TIP3P water model with
CHARMM36 force field to simulate the system.*


 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*

Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  


 

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Re: [gmx-users] Residue 'UNK' not found in residue topology database

[Navneet Kumar Singh]

Yes, I succeed in running NVT and NPT without any error. But when I
visualized the whole complex system (.gro) file in VMD/CHIMERA. It was like
(Please download .JPG from the below link)

https://fil.email/1pKxlHXy

I have attached a snapshot.
It looks like something weird problem with co-ordinates, 2 molecules are
connected with abnormal large bonds. These are the drug/small molecules.
What problem it can be ?

On Thu, Sep 12, 2019 at 11:29 PM Navneet Kumar Singh 
wrote:

> Yes, I succeed in running NVT and NPT without any error. But when I
> visualized the whole complex system (.gro) file in VMD/CHIMERA. It was like
>
> https://fil.email/1pKxlHXy
>
> I have attached a snapshot.
> It looks like something weird problem with co-ordinates, 2 molecules are
> connected with abnormal large bonds. These are the drug/small molecules.
> What problem it can be ?
>
>
>>
>>

-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  
<http://www.linkedin.com/in/navneet-kumar-74391814a/>
<http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>

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Re: [gmx-users] Residue 'UNK' not found in residue topology database

[Navneet Kumar Singh]

Thank You Sir!

I just removed the ligand part from the system.

Used Peptides+Water--Used pdb2gmx to create .gro file

converted the ligand.pdb in to .gro using command *gmx editconf -f unk.pdb
-o unk.gro*

combined the peptides+water.gro and ligand.gro to form complex.gro
updated the number of atoms.

Took a single UNK_fix.mol2 file and converted it to unk.itp file using the
method described in the protein-ligand complex tutorial at mdtutorials.com

Then updated the unk.itp and unk.prm file information in topol.top file.

Performed the energy minimization and everything went fine.

Sir is this right approach ?











On Sat, Sep 7, 2019 at 9:00 PM Justin Lemkul  wrote:

>
>
> On 9/7/19 10:28 AM, Navneet Kumar Singh wrote:
> > How to do this. I am using CHARMM36 force-field.
> >
> > Even if I follow " adding a new residue to force field" from GROMACS
> > documentation. I have to add/modify several things. Like .rtp files;.hdb
> > files; atomtypes.atp etc. But to add these new parameters in these files
> ?
>
> If you already have an .itp file for the ligand, it is as simple as
> removing the coordinates from the starting structure, generating the
> protein topology with pdb2gmx, adding an #include statement for the
> ligand .itp file, and specifying 10 of the ligand in [molecules].
>
> -Justin
>
> > On Sat, Sep 7, 2019 at 7:54 PM Navneet Kumar Singh  >
> > wrote:
> >
> >> I have 10 same ligands with different coordinates, as the ligands are
> >> randomly distributed around the box. Do I have to do it manually. Even
> the
> >> CGenFF will create the required .str files individually. How to deal
> with
> >> this. I have seen in research articles people are using different small
> >> molecules in different concentrations and simulate the whole system. I
> >> think it would good to introduce and define separate topology parameter
> for
> >> UNK. THen it will become a separate residue HETATM defined and pdb2gmx
> can
> >> automatically use this.
> >>
> >> On Sat, Sep 7, 2019 at 7:34 PM Bratin Kumar Das <
> >> 177cy500.bra...@nitk.edu.in> wrote:
> >>
> >>> You need to follow the procedure given in protein ligand
> system...Somehow
> >>> gromacs can't find the .itp file of the ligand which you added in your
> >>> topology file.
> >>>
> >>> On Sat 7 Sep, 2019, 6:24 PM Navneet Kumar Singh,  >
> >>> wrote:
> >>>
> >>>> Hello Everyone!
> >>>>
> >>>>
> >>>> I am trying to simulate 5 peptides, 10 small molecules (UNK) and
> water.
> >>>> I have used PACKMOL to make system having all these 3 ingredients.
> >>>> Peptides terminal residues were capped using ACE and NME in the pymol.
> >>>> It is pretty much straight forward simulating peptides with water as
> all
> >>>> necessary parameters are already defined.
> >>>> But When I am having UNK (A SMALL MOLECULE) in my system, its throwing
> >>>> error i.e. (Residue 'UNK' not found in residue topology database) and
> >>> this
> >>>> is pretty much obvious that pdb2gmx can't find any UNK.
> >>>>
> >>>> During protein-ligand simulations we first get the .gro files for
> >>> protein
> >>>> using pdb2gmx, similarly we prepare topology files for small molecules
> >>>> according to force field on some server or acpype. and then we combine
> >>> the
> >>>> .gro files of protein and ligand, simultaneously update the topology
> >>> files.
> >>>> then process continuous as usual.
> >>>>
> >>>> Here I have a .pdb file containing peptides and small molecules along
> >>> with
> >>>> water prepared using the PACKMOL.
> >>>> How to deal with ligand. I have processed the one ligand according
> >>> CHARMM
> >>>> force field (using CHARMM36 ) from CGenFF <
> >>> https://cgenff.umaryland.edu/>.
> >>>> I have all .itp, .prm and other files. But how to add and proceed
> >>> furthur?
> >>>>
> >>>>
> >>>>
> >>>>   Thanks & Regards
> >>>> ___
> >>>>
> >>>> [image: photo]
> >>>> *NAVNEET KUMAR*
> >>>>
> >>>> Doctoral Student
> >>>> Dept. of Pharmacoinformatics
> >>>> National I

Re: [gmx-users] Residue 'UNK' not found in residue topology database

[Navneet Kumar Singh]

How to do this. I am using CHARMM36 force-field.

Even if I follow " adding a new residue to force field" from GROMACS
documentation. I have to add/modify several things. Like .rtp files;.hdb
files; atomtypes.atp etc. But to add these new parameters in these files ?

On Sat, Sep 7, 2019 at 7:54 PM Navneet Kumar Singh 
wrote:

> I have 10 same ligands with different coordinates, as the ligands are
> randomly distributed around the box. Do I have to do it manually. Even the
> CGenFF will create the required .str files individually. How to deal with
> this. I have seen in research articles people are using different small
> molecules in different concentrations and simulate the whole system. I
> think it would good to introduce and define separate topology parameter for
> UNK. THen it will become a separate residue HETATM defined and pdb2gmx can
> automatically use this.
>
> On Sat, Sep 7, 2019 at 7:34 PM Bratin Kumar Das <
> 177cy500.bra...@nitk.edu.in> wrote:
>
>> You need to follow the procedure given in protein ligand system...Somehow
>> gromacs can't find the .itp file of the ligand which you added in your
>> topology file.
>>
>> On Sat 7 Sep, 2019, 6:24 PM Navneet Kumar Singh, 
>> wrote:
>>
>> > Hello Everyone!
>> >
>> >
>> > I am trying to simulate 5 peptides, 10 small molecules (UNK) and water.
>> > I have used PACKMOL to make system having all these 3 ingredients.
>> > Peptides terminal residues were capped using ACE and NME in the pymol.
>> > It is pretty much straight forward simulating peptides with water as all
>> > necessary parameters are already defined.
>> > But When I am having UNK (A SMALL MOLECULE) in my system, its throwing
>> > error i.e. (Residue 'UNK' not found in residue topology database) and
>> this
>> > is pretty much obvious that pdb2gmx can't find any UNK.
>> >
>> > During protein-ligand simulations we first get the .gro files for
>> protein
>> > using pdb2gmx, similarly we prepare topology files for small molecules
>> > according to force field on some server or acpype. and then we combine
>> the
>> > .gro files of protein and ligand, simultaneously update the topology
>> files.
>> > then process continuous as usual.
>> >
>> > Here I have a .pdb file containing peptides and small molecules along
>> with
>> > water prepared using the PACKMOL.
>> > How to deal with ligand. I have processed the one ligand according
>> CHARMM
>> > force field (using CHARMM36 ) from CGenFF <
>> https://cgenff.umaryland.edu/>.
>> > I have all .itp, .prm and other files. But how to add and proceed
>> furthur?
>> >
>> >
>> >
>> >
>> >  Thanks & Regards
>> > ___
>> >
>> > [image: photo]
>> > *NAVNEET KUMAR*
>> >
>> > Doctoral Student
>> > Dept. of Pharmacoinformatics
>> > National Institute of Pharmaceutical Education and Research, Sector 67,
>> > S.A.S. Nagar - 160062, Punjab (INDIA)
>> >
>> > E navneet...@gmail.com  
>> >
>> > <http://www.linkedin.com/in/navneet-kumar-74391814a/>
>> > <http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>
>> >
>> > Please consider your environmental responsibility. Before printing this
>> > e-mail message, ask yourself whether you really need a hard copy.
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
> --
>
>
>
>
>
>
>  Thanks & Regards
> ___
>
> [image: photo]
>

Re: [gmx-users] Residue 'UNK' not found in residue topology database

[Navneet Kumar Singh]

I have 10 same ligands with different coordinates, as the ligands are
randomly distributed around the box. Do I have to do it manually. Even the
CGenFF will create the required .str files individually. How to deal with
this. I have seen in research articles people are using different small
molecules in different concentrations and simulate the whole system. I
think it would good to introduce and define separate topology parameter for
UNK. THen it will become a separate residue HETATM defined and pdb2gmx can
automatically use this.

On Sat, Sep 7, 2019 at 7:34 PM Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
wrote:

> You need to follow the procedure given in protein ligand system...Somehow
> gromacs can't find the .itp file of the ligand which you added in your
> topology file.
>
> On Sat 7 Sep, 2019, 6:24 PM Navneet Kumar Singh, 
> wrote:
>
> > Hello Everyone!
> >
> >
> > I am trying to simulate 5 peptides, 10 small molecules (UNK) and water.
> > I have used PACKMOL to make system having all these 3 ingredients.
> > Peptides terminal residues were capped using ACE and NME in the pymol.
> > It is pretty much straight forward simulating peptides with water as all
> > necessary parameters are already defined.
> > But When I am having UNK (A SMALL MOLECULE) in my system, its throwing
> > error i.e. (Residue 'UNK' not found in residue topology database) and
> this
> > is pretty much obvious that pdb2gmx can't find any UNK.
> >
> > During protein-ligand simulations we first get the .gro files for protein
> > using pdb2gmx, similarly we prepare topology files for small molecules
> > according to force field on some server or acpype. and then we combine
> the
> > .gro files of protein and ligand, simultaneously update the topology
> files.
> > then process continuous as usual.
> >
> > Here I have a .pdb file containing peptides and small molecules along
> with
> > water prepared using the PACKMOL.
> > How to deal with ligand. I have processed the one ligand according CHARMM
> > force field (using CHARMM36 ) from CGenFF <https://cgenff.umaryland.edu/
> >.
> > I have all .itp, .prm and other files. But how to add and proceed
> furthur?
> >
> >
> >
> >
> >  Thanks & Regards
> > ___
> >
> > [image: photo]
> > *NAVNEET KUMAR*
> >
> > Doctoral Student
> > Dept. of Pharmacoinformatics
> > National Institute of Pharmaceutical Education and Research, Sector 67,
> > S.A.S. Nagar - 160062, Punjab (INDIA)
> >
> > E navneet...@gmail.com  
> >
> > <http://www.linkedin.com/in/navneet-kumar-74391814a/>
> > <http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>
> >
> > Please consider your environmental responsibility. Before printing this
> > e-mail message, ask yourself whether you really need a hard copy.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>


-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  
<http://www.linkedin.com/in/navneet-kumar-74391814a/>
<http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
Gromacs Users mailing list

* Please search the archive at 
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[gmx-users] Residue 'UNK' not found in residue topology database

[Navneet Kumar Singh]

Hello Everyone!


I am trying to simulate 5 peptides, 10 small molecules (UNK) and water.
I have used PACKMOL to make system having all these 3 ingredients.
Peptides terminal residues were capped using ACE and NME in the pymol.
It is pretty much straight forward simulating peptides with water as all
necessary parameters are already defined.
But When I am having UNK (A SMALL MOLECULE) in my system, its throwing
error i.e. (Residue 'UNK' not found in residue topology database) and this
is pretty much obvious that pdb2gmx can't find any UNK.

During protein-ligand simulations we first get the .gro files for protein
using pdb2gmx, similarly we prepare topology files for small molecules
according to force field on some server or acpype. and then we combine the
.gro files of protein and ligand, simultaneously update the topology files.
then process continuous as usual.

Here I have a .pdb file containing peptides and small molecules along with
water prepared using the PACKMOL.
How to deal with ligand. I have processed the one ligand according CHARMM
force field (using CHARMM36 ) from CGenFF .
I have all .itp, .prm and other files. But how to add and proceed furthur?




 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*

Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)

E navneet...@gmail.com  


 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] Fatal error: Atom O4 in residue GLU 7 was not found in rtp entry

[Navneet Kumar Singh]

Yeah!

But I don't want any charge at terminal residues. I think I should cap
these by acetyl or amide moiety. Let me try this.

On Fri, 6 Sep 2019, 19:45 Justin Lemkul,  wrote:

>
>
> On 9/6/19 4:32 AM, Navneet Kumar Singh wrote:
> > Hello Everyone!
> >
> > I am trying to simulate five peptides along with water using GROMACS.
> > I have used the PACKMOL to prepare initail PDB files.
> > Peptide were made using Schrodinger Maestro.
> > I have got a final PDB file having the water molecules and randowmly
> > distributed peptides.
> >
> >
> > After that I am using command pdb2gmx using the CHARMM36 force field.
> >
> > Following are the commands and its output,
> >
> >
> -
> > gmx pdb2gmx -f final.pdb -o final.gro -water spce -ignh -ter
> >   :-) GROMACS - gmx pdb2gmx, 2018.4 (-:
> >
> >  GROMACS is written by:
> >   Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C.
> > Berendsen
> >  Par BjelkmarAldert van Buuren   Rudi van Drunen Anton
> Feenstra
> >Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca
> Hamuraru
> >   Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri
> Kraus
> >
> >Carsten Kutzner  Per Larsson  Justin A. LemkulViveca
> Lindahl
> >Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu
> Murtola
> >  Szilard Pall   Sander Pronk  Roland Schulz Alexey
> Shvetsov
> > Michael Shirts Alfons Sijbers Peter TielemanTeemu
> Virolainen
> >   Christian WennbergMaarten Wolf
> > and the project leaders:
> >  Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> >
> > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> > Copyright (c) 2001-2017, The GROMACS development team at
> > Uppsala University, Stockholm University and
> > the Royal Institute of Technology, Sweden.
> > check out http://www.gromacs.org for more information.
> >
> > GROMACS is free software; you can redistribute it and/or modify it
> > under the terms of the GNU Lesser General Public License
> > as published by the Free Software Foundation; either version 2.1
> > of the License, or (at your option) any later version.
> >
> > GROMACS:  gmx pdb2gmx, version 2018.4
> > Executable:   /usr/local/gromacs/bin/gmx
> > Data prefix:  /usr/local/gromacs
> > Working dir:  /home/navneet/Desktop/amyloid
> > Command line:
> >gmx pdb2gmx -f final.pdb -o final.gro -water spce -ignh -ter
> >
> >
> > Select the Force Field:
> >  From current directory:
> >   1: CHARMM36 all-atom force field (March 2019)
> >  From '/usr/local/gromacs/share/gromacs/top':
> >   2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
> > 1999-2012, 2003)
> >   3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
> >   4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res.
> 29,
> > 461-469, 1996)
> >   5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
> > 1049-1074, 2000)
> >   6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
> > 712-725, 2006)
> >   7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
> > Proteins 78, 1950-58, 2010)
> >   8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
> >   9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
> > 10: GROMOS96 43a1 force field
> > 11: GROMOS96 43a2 force field (improved alkane dihedrals)
> > 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> > 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> > 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> > 15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856,
> DOI:
> > 10.1007/s00249-011-0700-9)
> > 16: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856,
> DOI:
> > 10.1007/s00249-011-0700-9)
> > 17: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856,
> DOI:
> > 10.1007/s00249-011-0700-9)
> > 18: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> > 1
> >
> > Using the Charmm36-mar2019 force field in directory ./charmm36-mar2019.ff
> >
> > Opening force field file ./charmm36-mar2019.ff/merged.r2b
> > Reading final.pdb...
> > Read 'Built with Pac

[gmx-users] Fatal error: Atom O4 in residue GLU 7 was not found in rtp entry

[Navneet Kumar Singh]

Hello Everyone!

I am trying to simulate five peptides along with water using GROMACS.
I have used the PACKMOL to prepare initail PDB files.
Peptide were made using Schrodinger Maestro.
I have got a final PDB file having the water molecules and randowmly
distributed peptides.


After that I am using command pdb2gmx using the CHARMM36 force field.

Following are the commands and its output,

-
gmx pdb2gmx -f final.pdb -o final.gro -water spce -ignh -ter
 :-) GROMACS - gmx pdb2gmx, 2018.4 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C.
Berendsen
Par BjelkmarAldert van Buuren   Rudi van Drunen Anton Feenstra
  Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca Hamuraru
 Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus

  Carsten Kutzner  Per Larsson  Justin A. LemkulViveca Lindahl
  Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu Murtola
Szilard Pall   Sander Pronk  Roland Schulz Alexey Shvetsov
   Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen
 Christian WennbergMaarten Wolf
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx pdb2gmx, version 2018.4
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/navneet/Desktop/amyloid
Command line:
  gmx pdb2gmx -f final.pdb -o final.gro -water spce -ignh -ter


Select the Force Field:
>From current directory:
 1: CHARMM36 all-atom force field (March 2019)
>From '/usr/local/gromacs/share/gromacs/top':
 2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
1999-2012, 2003)
 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29,
461-469, 1996)
 5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
1049-1074, 2000)
 6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
712-725, 2006)
 7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
Proteins 78, 1950-58, 2010)
 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
10.1007/s00249-011-0700-9)
16: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
10.1007/s00249-011-0700-9)
17: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
10.1007/s00249-011-0700-9)
18: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
1

Using the Charmm36-mar2019 force field in directory ./charmm36-mar2019.ff

Opening force field file ./charmm36-mar2019.ff/merged.r2b
Reading final.pdb...
Read 'Built with Packmol through Packmol Memgen', 5305 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 1 blocks of water and 5035 residues with 5305 atoms

  chain  #res #atoms
  1 'A'35305
  2 ' '  5000   5000  (only water)


WARNING: there were 5000 atoms with zero occupancy and 0 atoms with
 occupancy unequal to one (out of 5305 atoms). Check your pdb file.

Opening force field file ./charmm36-mar2019.ff/atomtypes.atp
Atomtype 447
Reading residue database... (charmm36-mar2019)
Opening force field file ./charmm36-mar2019.ff/merged.rtp
Residue 1318
Sorting it all out...
Opening force field file ./charmm36-mar2019.ff/merged.hdb
Opening force field file ./charmm36-mar2019.ff/merged.n.tdb
Opening force field file ./charmm36-mar2019.ff/merged.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 'A' (305 atoms, 35 residues)
Identified residue LYS1 as a starting terminus.
Identified residue GLU7 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for LYS-1
 0: NH3+
 1: NH2
 2: 5TER
 3: None
1
Start terminus LYS-1: NH2
Select end terminus type for GLU-7

Re: [gmx-users] HtoD cudaMemcpyAsync failed: invalid argument

[Navneet Kumar Singh]

Yeah -nb cpu
Running on cpu.

On Thu, 29 Aug 2019, 17:33 Mark Abraham,  wrote:

> Hi,
>
> Did you try doing em with the flag I mentioned? Simulation won't need any
> change.
>
> Mark
>
> On Mon., 26 Aug. 2019, 22:25 Navneet Kumar Singh, 
> wrote:
>
> > Thank You Sir.
> >
> > Again installed gromacs2016.6 (final version from gromacs2016.x).
> > Throwing same error(HtoD cudaMemcpyAsync failed: invalid argument)
> >
> > . Its running on CPU, but not on GPU. Work of 3 days will take 15 days.
> > Already completed simulation for other complexes. This complex creating
> > problem due to vsites3. PLEASE HELP DEADLINE IS APPROACHING.
> >
> > On Tue, Aug 27, 2019 at 12:23 AM Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > If you have a reason to have to use 2016.x, then please get the latest
> > > version (which is always advisable when starting new work) because this
> > > issue is fixed there. You also don't have to run energy minimization on
> > > GPUs, so you could just append -nb cpu to your mdrun command line to
> > avoid
> > > the problem.
> > >
> > > Mark
> > >
> > > On Mon, 26 Aug 2019 at 20:44, Navneet Kumar Singh <
> navneet...@gmail.com>
> > > wrote:
> > >
> > > > Currently I am using only gromacs16.5. As this have *"PLEASE NOTE*
> that
> > > the
> > > > current versions do support lone pair construction on halogens,
> however
> > > the
> > > > current construction is only compatible with GROMACS-2016.x and by
> > using
> > > > gmx grompp -maxwarn 1 to override the warning about lone pair
> > > > construction."
> > > >
> > > > I was unable to understand this "For all other GROMACS versions, you
> > will
> > > > have to manually edit the topology to use "3fad" construction and
> > > > appropriate atom numbers."as I was using 2018.4. So I switched to
> > > > version-16. But now trapped in this HtoD cudaMemcpyAsync failed:
> > invalid
> > > > argumenterror.
> > > >
> > > > On Tue, Aug 27, 2019 at 12:09 AM Mark Abraham <
> > mark.j.abra...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > You're running 2016.x which had a bug, not the 2018.x you thought
> you
> > > > were
> > > > > using. Use GMXRC or your cluster's modules to select the version
> you
> > > want
> > > > > to use in the terminal or script that you want to use.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Mon, 26 Aug 2019 at 20:34, Navneet Kumar Singh <
> > > navneet...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > What kind of error is this. Previously Gromacs 2018.4 version was
> > > > running
> > > > > > fine using GPU. But Now this error I am getting.
> > > > > >
> > > > > > _
> > > > > >
> > > > > > gmx mdrun -v -deffnm em
> > > > > >   :-) GROMACS - gmx mdrun, 2016.5 (-:
> > > > > >
> > > > > > GROMACS is written by:
> > > > > >  Emile Apol  Rossen Apostolov  Herman J.C. Berendsen
> Par
> > > > > > Bjelkmar
> > > > > >  Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit
> > > > > Groenhof
> > > > > >  Christoph Junghans   Anca HamuraruVincent Hindriksen
> Dimitrios
> > > > > > Karkoulis
> > > > > > Peter KassonJiri Kraus  Carsten Kutzner  Per
> > > > Larsson
> > > > > >   Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik
> > > > Marklund
> > > > > >Teemu Murtola   Szilard Pall   Sander Pronk
> Roland
> > > > Schulz
> > > > > >   Alexey Shvetsov Michael Shirts Alfons Sijbers Peter
> > > > > Tieleman
> > > > > >   Teemu Virolainen  Christian WennbergMaarten Wolf
> > > > > >and the project leaders:
> > > > > > Mark Abraham, Berk Hess, Erik Lindahl, and David van der
> > > Spoel
> > > > &

[gmx-users] Gromacs /MMPBSA Calculation

[Navneet Kumar Singh]

Hello Gromacs Developers/ Users

Which tool you use to calculate binding free energy for the trajectory file
obtained from gromacs ?I have used g_mmpbsa (
https://rashmikumari.github.io/g_mmpbsa), but at many instances it gives
either positive or high negative binding energy which makes difficult any
sort of comparison. Solute dielectric constant is said to be a variable
which is responsible for this error. Suggestions/solutions please.
-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
Gromacs Users mailing list

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Re: [gmx-users] HtoD cudaMemcpyAsync failed: invalid argument

[Navneet Kumar Singh]

Thank You Sir.

Again installed gromacs2016.6 (final version from gromacs2016.x).
Throwing same error(HtoD cudaMemcpyAsync failed: invalid argument)

. Its running on CPU, but not on GPU. Work of 3 days will take 15 days.
Already completed simulation for other complexes. This complex creating
problem due to vsites3. PLEASE HELP DEADLINE IS APPROACHING.

On Tue, Aug 27, 2019 at 12:23 AM Mark Abraham 
wrote:

> Hi,
>
> If you have a reason to have to use 2016.x, then please get the latest
> version (which is always advisable when starting new work) because this
> issue is fixed there. You also don't have to run energy minimization on
> GPUs, so you could just append -nb cpu to your mdrun command line to avoid
> the problem.
>
> Mark
>
> On Mon, 26 Aug 2019 at 20:44, Navneet Kumar Singh 
> wrote:
>
> > Currently I am using only gromacs16.5. As this have *"PLEASE NOTE* that
> the
> > current versions do support lone pair construction on halogens, however
> the
> > current construction is only compatible with GROMACS-2016.x and by using
> > gmx grompp -maxwarn 1 to override the warning about lone pair
> > construction."
> >
> > I was unable to understand this "For all other GROMACS versions, you will
> > have to manually edit the topology to use "3fad" construction and
> > appropriate atom numbers."as I was using 2018.4. So I switched to
> > version-16. But now trapped in this HtoD cudaMemcpyAsync failed: invalid
> > argumenterror.
> >
> > On Tue, Aug 27, 2019 at 12:09 AM Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > You're running 2016.x which had a bug, not the 2018.x you thought you
> > were
> > > using. Use GMXRC or your cluster's modules to select the version you
> want
> > > to use in the terminal or script that you want to use.
> > >
> > > Mark
> > >
> > > On Mon, 26 Aug 2019 at 20:34, Navneet Kumar Singh <
> navneet...@gmail.com>
> > > wrote:
> > >
> > > > What kind of error is this. Previously Gromacs 2018.4 version was
> > running
> > > > fine using GPU. But Now this error I am getting.
> > > >
> > > > _
> > > >
> > > > gmx mdrun -v -deffnm em
> > > >   :-) GROMACS - gmx mdrun, 2016.5 (-:
> > > >
> > > > GROMACS is written by:
> > > >  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> > > > Bjelkmar
> > > >  Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit
> > > Groenhof
> > > >  Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
> > > > Karkoulis
> > > > Peter KassonJiri Kraus  Carsten Kutzner  Per
> > Larsson
> > > >   Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik
> > Marklund
> > > >Teemu Murtola   Szilard Pall   Sander Pronk  Roland
> > Schulz
> > > >   Alexey Shvetsov Michael Shirts Alfons Sijbers Peter
> > > Tieleman
> > > >   Teemu Virolainen  Christian WennbergMaarten Wolf
> > > >and the project leaders:
> > > > Mark Abraham, Berk Hess, Erik Lindahl, and David van der
> Spoel
> > > >
> > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> > > > Copyright (c) 2001-2017, The GROMACS development team at
> > > > Uppsala University, Stockholm University and
> > > > the Royal Institute of Technology, Sweden.
> > > > check out http://www.gromacs.org for more information.
> > > >
> > > > GROMACS is free software; you can redistribute it and/or modify it
> > > > under the terms of the GNU Lesser General Public License
> > > > as published by the Free Software Foundation; either version 2.1
> > > > of the License, or (at your option) any later version.
> > > >
> > > > GROMACS:  gmx mdrun, version 2016.5
> > > > Executable:   /usr/local/gromacs/bin/gmx
> > > > Data prefix:  /usr/local/gromacs
> > > > Working dir:  /home/nitttr/Desktop/Hydroxy_chloroquine
> > > > Command line:
> > > >   gmx mdrun -v -deffnm em
> > > >
> > > >
> > > > Back Off! I just backed up em.log to ./#em.log.7#
> > > >
> > > > Running on 1 node with total 16 cores, 32 logical cores, 1 compati

Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

I have seen this in Gromacs manual.

[ virtual_sites2 ]
; Site  fromfunct  a
5   1 2 1  0.7439756

for type 3 like this:

[ virtual_sites3 ]
; Site  from   funct   a  b
5   1 2 3  1   0.7439756  0.128012

for type 3fd like this:

[ virtual_sites3 ]
; Site  from   funct   a  d
5   1 2 3  2   0.5-0.105

for type 3fad like this:

[ virtual_sites3 ]
; Site  from   funct   theta  d
5   1 2 3  3   1200.5

for type 3out like this:

[ virtual_sites3 ]
; Site  from   funct   a  b  c
5   1 2 3  4   -0.4   -0.4   6.9281

for type 4fdn like this:

[ virtual_sites4 ]
; Site  from  funct   a  b  c
5   1 2 3 4   2   1.00.9   0.105

__


I have this from unk.itp file.

[ virtual_sites3 ]
; Site   from funct a   d
   52 12323 2 0   -0.164

[ exclusions ]
; ai  aj
152 1
   5223 1
   5221 1
   5222 1
   5218 1
   5219 1
   5251 1
   5250 1


Now I have to add this in topology file. Is this supposed to add in
system.top ?

On Tue, Aug 27, 2019 at 12:11 AM Justin Lemkul  wrote:

>
>
> On 8/26/19 2:33 PM, Navneet Kumar Singh wrote:
> > I can't understand meaning of this "For all other GROMACS versions, you
> > will have to manually edit the topology to use "3fad" construction and
> > appropriate atom numbers." If I am using version other than the
> > Gromacs2016.x.
> >
> > Can I get example of any topology file where these kind of
> construction've
> > for loan pair done manually in the topology file?
>
> Please see the manual for examples of what the different construction
> types are.
>
> -Justin
>
> > On Mon, Aug 26, 2019 at 11:57 PM Justin Lemkul  wrote:
> >
> >>
> >> On 8/26/19 1:14 PM, Navneet Kumar Singh wrote:
> >>> Do I have to add vsite3 information from unk.itp to system.top files?
> >> That directive belongs in the topology to which it corresponds. If it is
> >> in unk.itp, then it is already in system.top. You don't need to include
> >> anything else.
> >>
> >> -Justin
> >>
> >>> -maxwarn 1 flag I checked in gromacs 16 version and it's running there.
> >>>
> >>> On Mon, 26 Aug 2019, 00:58 Justin Lemkul,  wrote:
> >>>
> >>>> On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:
> >>>>> Yeah! I have read that.
> >>>>>
> >>>>> uses -maxwarn 1 to produce .tpr file using grompp command as
> mentioned
> >> in
> >>>> Since you are getting an error rather than a warning, that means you
> are
> >>>> not using GROMACS 2016.x, as the instructions I pointed to you say.
> >>>>
> >>>> If you want to use a different GROMACS version, you have to change the
> >>>> topology. Again see the link I provided for a description of what to
> do.
> >>>>
> >>>> -Justin
> >>>>
> >>>>> python script cgenff_charmm2gmx_py2.py
> >>>>>
> >>>>> output of cgenff_charmm2gmx_py2.py
> >>>>>
> >>
> _
> >>>>> NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16
> (default,
> >>>> Mar
> >>>>> 26 2019, 10:00:46)
> >>>>> [GCC 5.4.0 20160609]
> >>>>>
> >>>>> NOTE 2: Please be sure to use the same version of CGenFF in your
> >>>>> simulations that was used during parameter generation:
> >>>>> --Version of CGenFF detected in  unk.str : 4.0
> >>>>> --Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc :
> >> 4.0
> >>>>> NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
> >>>>> parameters that are already in CGenFF' option when uploading a
> molecule
> >>>>> into CGenFF.
> >>>>>
> >>>>> NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.
> >>>

Re: [gmx-users] HtoD cudaMemcpyAsync failed: invalid argument

[Navneet Kumar Singh]

Currently I am using only gromacs16.5. As this have *"PLEASE NOTE* that the
current versions do support lone pair construction on halogens, however the
current construction is only compatible with GROMACS-2016.x and by using
gmx grompp -maxwarn 1 to override the warning about lone pair construction."

I was unable to understand this "For all other GROMACS versions, you will
have to manually edit the topology to use "3fad" construction and
appropriate atom numbers."as I was using 2018.4. So I switched to
version-16. But now trapped in this HtoD cudaMemcpyAsync failed: invalid
argumenterror.

On Tue, Aug 27, 2019 at 12:09 AM Mark Abraham 
wrote:

> Hi,
>
> You're running 2016.x which had a bug, not the 2018.x you thought you were
> using. Use GMXRC or your cluster's modules to select the version you want
> to use in the terminal or script that you want to use.
>
> Mark
>
> On Mon, 26 Aug 2019 at 20:34, Navneet Kumar Singh 
> wrote:
>
> > What kind of error is this. Previously Gromacs 2018.4 version was running
> > fine using GPU. But Now this error I am getting.
> >
> > _
> >
> > gmx mdrun -v -deffnm em
> >   :-) GROMACS - gmx mdrun, 2016.5 (-:
> >
> > GROMACS is written by:
> >  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> > Bjelkmar
> >  Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit
> Groenhof
> >  Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
> > Karkoulis
> > Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
> >   Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik Marklund
> >Teemu Murtola   Szilard Pall   Sander Pronk  Roland Schulz
> >   Alexey Shvetsov Michael Shirts Alfons Sijbers Peter
> Tieleman
> >   Teemu Virolainen  Christian WennbergMaarten Wolf
> >and the project leaders:
> > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> >
> > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> > Copyright (c) 2001-2017, The GROMACS development team at
> > Uppsala University, Stockholm University and
> > the Royal Institute of Technology, Sweden.
> > check out http://www.gromacs.org for more information.
> >
> > GROMACS is free software; you can redistribute it and/or modify it
> > under the terms of the GNU Lesser General Public License
> > as published by the Free Software Foundation; either version 2.1
> > of the License, or (at your option) any later version.
> >
> > GROMACS:  gmx mdrun, version 2016.5
> > Executable:   /usr/local/gromacs/bin/gmx
> > Data prefix:  /usr/local/gromacs
> > Working dir:  /home/nitttr/Desktop/Hydroxy_chloroquine
> > Command line:
> >   gmx mdrun -v -deffnm em
> >
> >
> > Back Off! I just backed up em.log to ./#em.log.7#
> >
> > Running on 1 node with total 16 cores, 32 logical cores, 1 compatible GPU
> > Hardware detected:
> >   CPU info:
> > Vendor: Intel
> > Brand:  Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
> > SIMD instructions most likely to fit this hardware: AVX_512
> > SIMD instructions selected at GROMACS compile time: AVX_512
> >
> >   Hardware topology: Basic
> >   GPU info:
> > Number of GPUs detected: 1
> > #0: NVIDIA Tesla P4, compute cap.: 6.1, ECC: yes, stat: compatible
> >
> > Reading file em.tpr, VERSION 2016.5 (single precision)
> > Using 1 MPI thread
> > Using 32 OpenMP threads
> >
> > 1 compatible GPU is present, with ID 0
> > 1 GPU auto-selected for this run.
> > Mapping of GPU ID to the 1 PP rank in this node: 0
> >
> > Application clocks (GPU clocks) for Tesla P4 are (3003,1531)
> >
> > Back Off! I just backed up em.trr to ./#em.trr.7#
> >
> > Back Off! I just backed up em.edr to ./#em.edr.7#
> >
> > Steepest Descents:
> >Tolerance (Fmax)   =  1.0e+03
> >Number of steps=5
> >
> > ---
> > Program: gmx mdrun, version 2016.5
> > Source file: src/gromacs/gpu_utils/cudautils.cu (line 105)
> >
> > Fatal error:
> > HtoD cudaMemcpyAsync failed: invalid argument
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ---
> &g

Re: [gmx-users] HtoD cudaMemcpyAsync failed: invalid argument

[Navneet Kumar Singh]

This is make check reuslt


100% tests passed, 0 tests failed out of 27

Label Time Summary:
GTest =   1.24 sec*proc (18 tests)
IntegrationTest   =   5.93 sec*proc (2 tests)
MpiIntegrationTest=   0.44 sec*proc (1 test)
UnitTest  =   1.24 sec*proc (18 tests)

Total Test time (real) = 204.82 sec
[100%] Built target run-ctest
[100%] Built target check
___

Meaning installation was fine.

I have used gcc-6 as previously it was throwing error not to use gcc
version latter than than 6.0 .

On Tue, Aug 27, 2019 at 12:00 AM Navneet Kumar Singh 
wrote:

> What kind of error is this. Previously Gromacs 2018.4 version was running
> fine using GPU. But Now this error I am getting.
>
> _
>
> gmx mdrun -v -deffnm em
>   :-) GROMACS - gmx mdrun, 2016.5 (-:
>
> GROMACS is written by:
>  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> Bjelkmar
>  Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit Groenhof
>
>  Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
> Karkoulis
> Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
>
>   Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik Marklund
>
>Teemu Murtola   Szilard Pall   Sander Pronk  Roland Schulz
>
>   Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
>
>   Teemu Virolainen  Christian WennbergMaarten Wolf
>and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2017, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
>
> GROMACS:  gmx mdrun, version 2016.5
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Working dir:  /home/nitttr/Desktop/Hydroxy_chloroquine
> Command line:
>   gmx mdrun -v -deffnm em
>
>
> Back Off! I just backed up em.log to ./#em.log.7#
>
> Running on 1 node with total 16 cores, 32 logical cores, 1 compatible GPU
> Hardware detected:
>   CPU info:
> Vendor: Intel
> Brand:  Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
> SIMD instructions most likely to fit this hardware: AVX_512
> SIMD instructions selected at GROMACS compile time: AVX_512
>
>   Hardware topology: Basic
>   GPU info:
> Number of GPUs detected: 1
> #0: NVIDIA Tesla P4, compute cap.: 6.1, ECC: yes, stat: compatible
>
> Reading file em.tpr, VERSION 2016.5 (single precision)
> Using 1 MPI thread
> Using 32 OpenMP threads
>
> 1 compatible GPU is present, with ID 0
> 1 GPU auto-selected for this run.
> Mapping of GPU ID to the 1 PP rank in this node: 0
>
> Application clocks (GPU clocks) for Tesla P4 are (3003,1531)
>
> Back Off! I just backed up em.trr to ./#em.trr.7#
>
> Back Off! I just backed up em.edr to ./#em.edr.7#
>
> Steepest Descents:
>Tolerance (Fmax)   =  1.0e+03
>Number of steps=5
>
> ---
> Program: gmx mdrun, version 2016.5
> Source file: src/gromacs/gpu_utils/cudautils.cu (line 105)
>
> Fatal error:
> HtoD cudaMemcpyAsync failed: invalid argument
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> --
>
>
>
>
>
>
>  Thanks & Regards
> ___
>
> [image: photo]
> *NAVNEET KUMAR*
> Doctoral Student
> Dept. of Pharmacoinformatics
> National Institute of Pharmaceutical Education and Research, Sector 67,
> S.A.S. Nagar - 160062, Punjab (INDIA)
> P +918017967647  <+918017967647> |
> E navneet...@gmail.com  
> <http://www.linkedin.com/in/navneet-kumar-74391814a/>
> <http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>
>
> Please consider your environmental responsibility. Before printing this
> e-mail message,

Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

I can't understand meaning of this "For all other GROMACS versions, you
will have to manually edit the topology to use "3fad" construction and
appropriate atom numbers." If I am using version other than the
Gromacs2016.x.

Can I get example of any topology file where these kind of construction've
for loan pair done manually in the topology file?

On Mon, Aug 26, 2019 at 11:57 PM Justin Lemkul  wrote:

>
>
> On 8/26/19 1:14 PM, Navneet Kumar Singh wrote:
> > Do I have to add vsite3 information from unk.itp to system.top files?
>
> That directive belongs in the topology to which it corresponds. If it is
> in unk.itp, then it is already in system.top. You don't need to include
> anything else.
>
> -Justin
>
> > -maxwarn 1 flag I checked in gromacs 16 version and it's running there.
> >
> > On Mon, 26 Aug 2019, 00:58 Justin Lemkul,  wrote:
> >
> >>
> >> On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:
> >>> Yeah! I have read that.
> >>>
> >>> uses -maxwarn 1 to produce .tpr file using grompp command as mentioned
> in
> >> Since you are getting an error rather than a warning, that means you are
> >> not using GROMACS 2016.x, as the instructions I pointed to you say.
> >>
> >> If you want to use a different GROMACS version, you have to change the
> >> topology. Again see the link I provided for a description of what to do.
> >>
> >> -Justin
> >>
> >>> python script cgenff_charmm2gmx_py2.py
> >>>
> >>> output of cgenff_charmm2gmx_py2.py
> >>>
> >>
> _
> >>> NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default,
> >> Mar
> >>> 26 2019, 10:00:46)
> >>> [GCC 5.4.0 20160609]
> >>>
> >>> NOTE 2: Please be sure to use the same version of CGenFF in your
> >>> simulations that was used during parameter generation:
> >>> --Version of CGenFF detected in  unk.str : 4.0
> >>> --Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc :
> 4.0
> >>>
> >>> NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
> >>> parameters that are already in CGenFF' option when uploading a molecule
> >>> into CGenFF.
> >>>
> >>> NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.
> >> This
> >>> is not a problem, just FYI!
> >>>
> >>>  DONE 
> >>> Conversion complete.
> >>> The molecule topology has been written to unk.itp
> >>> Additional parameters needed by the molecule are written to unk.prm,
> >> which
> >>> needs to be included in the system .top
> >>>
> >>> PLEASE NOTE: lone pair construction requires duplicate host atom
> numbers,
> >>> which will make grompp complain
> >>> To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this
> >> check
> >>
> 
> >>> After that I am using same -maxwarn 1 but still, it's giving error. It
> >> may
> >>> be some silly mistake please let me know.
> >>>
> >>>
> >>> On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:
> >>>
> >>>> On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:
> >>>>> Thank You Sir!
> >>>>>
> >>>>> Attached file can be downloaded from following link.
> >>>>>
> >>>>> https://fil.email/OR7Nsh0f
> >>>>> <https://fil.email/OR7Nsh0f?&showconfirmation=true>
> >>>>> 
> >>>>> Error
> >>>>>
> >>>>> ERROR 1 [file unk.itp, line 497]:
> >>>>>  Duplicate atom index (23) in virtual_sites3
> >>>>> ___
> >>>>>
> >>>>> It support lone pair construction for halogens only. Please suggest
> >> some
> >>>>> alternatives.
> >>>> The link I provided before describes what you need to do. Please
> consult
> >>>> tha

[gmx-users] HtoD cudaMemcpyAsync failed: invalid argument

[Navneet Kumar Singh]

What kind of error is this. Previously Gromacs 2018.4 version was running
fine using GPU. But Now this error I am getting.

_

gmx mdrun -v -deffnm em
  :-) GROMACS - gmx mdrun, 2016.5 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar
 Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit Groenhof
 Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
Karkoulis
Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
  Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik Marklund
   Teemu Murtola   Szilard Pall   Sander Pronk  Roland Schulz
  Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
  Teemu Virolainen  Christian WennbergMaarten Wolf
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx mdrun, version 2016.5
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/nitttr/Desktop/Hydroxy_chloroquine
Command line:
  gmx mdrun -v -deffnm em


Back Off! I just backed up em.log to ./#em.log.7#

Running on 1 node with total 16 cores, 32 logical cores, 1 compatible GPU
Hardware detected:
  CPU info:
Vendor: Intel
Brand:  Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
SIMD instructions most likely to fit this hardware: AVX_512
SIMD instructions selected at GROMACS compile time: AVX_512

  Hardware topology: Basic
  GPU info:
Number of GPUs detected: 1
#0: NVIDIA Tesla P4, compute cap.: 6.1, ECC: yes, stat: compatible

Reading file em.tpr, VERSION 2016.5 (single precision)
Using 1 MPI thread
Using 32 OpenMP threads

1 compatible GPU is present, with ID 0
1 GPU auto-selected for this run.
Mapping of GPU ID to the 1 PP rank in this node: 0

Application clocks (GPU clocks) for Tesla P4 are (3003,1531)

Back Off! I just backed up em.trr to ./#em.trr.7#

Back Off! I just backed up em.edr to ./#em.edr.7#

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5

---
Program: gmx mdrun, version 2016.5
Source file: src/gromacs/gpu_utils/cudautils.cu (line 105)

Fatal error:
HtoD cudaMemcpyAsync failed: invalid argument

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
Gromacs Users mailing list

* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

Do I have to add vsite3 information from unk.itp to system.top files?

-maxwarn 1 flag I checked in gromacs 16 version and it's running there.

On Mon, 26 Aug 2019, 00:58 Justin Lemkul,  wrote:

>
>
> On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:
> > Yeah! I have read that.
> >
> > uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in
>
> Since you are getting an error rather than a warning, that means you are
> not using GROMACS 2016.x, as the instructions I pointed to you say.
>
> If you want to use a different GROMACS version, you have to change the
> topology. Again see the link I provided for a description of what to do.
>
> -Justin
>
> > python script cgenff_charmm2gmx_py2.py
> >
> > output of cgenff_charmm2gmx_py2.py
> >
> _
> >
> > NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default,
> Mar
> > 26 2019, 10:00:46)
> > [GCC 5.4.0 20160609]
> >
> > NOTE 2: Please be sure to use the same version of CGenFF in your
> > simulations that was used during parameter generation:
> > --Version of CGenFF detected in  unk.str : 4.0
> > --Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc : 4.0
> >
> > NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
> > parameters that are already in CGenFF' option when uploading a molecule
> > into CGenFF.
> >
> > NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.
> This
> > is not a problem, just FYI!
> >
> >  DONE 
> > Conversion complete.
> > The molecule topology has been written to unk.itp
> > Additional parameters needed by the molecule are written to unk.prm,
> which
> > needs to be included in the system .top
> >
> > PLEASE NOTE: lone pair construction requires duplicate host atom numbers,
> > which will make grompp complain
> > To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this
> check
> >
> ________
> >
> > After that I am using same -maxwarn 1 but still, it's giving error. It
> may
> > be some silly mistake please let me know.
> >
> >
> > On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:
> >
> >>
> >> On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:
> >>> Thank You Sir!
> >>>
> >>> Attached file can be downloaded from following link.
> >>>
> >>> https://fil.email/OR7Nsh0f
> >>> <https://fil.email/OR7Nsh0f?&showconfirmation=true>
> >>> 
> >>> Error
> >>>
> >>> ERROR 1 [file unk.itp, line 497]:
> >>> Duplicate atom index (23) in virtual_sites3
> >>> ___
> >>>
> >>> It support lone pair construction for halogens only. Please suggest
> some
> >>> alternatives.
> >> The link I provided before describes what you need to do. Please consult
> >> that information.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Off

Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

Yeah! I have read that.

uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in
python script cgenff_charmm2gmx_py2.py

output of cgenff_charmm2gmx_py2.py
_

NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default, Mar
26 2019, 10:00:46)
[GCC 5.4.0 20160609]

NOTE 2: Please be sure to use the same version of CGenFF in your
simulations that was used during parameter generation:
--Version of CGenFF detected in  unk.str : 4.0
--Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc : 4.0

NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
parameters that are already in CGenFF' option when uploading a molecule
into CGenFF.

NOTE 4: 1 lone pairs found in topology that are not in the mol2 file. This
is not a problem, just FYI!

 DONE 
Conversion complete.
The molecule topology has been written to unk.itp
Additional parameters needed by the molecule are written to unk.prm, which
needs to be included in the system .top

PLEASE NOTE: lone pair construction requires duplicate host atom numbers,
which will make grompp complain
To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this check


After that I am using same -maxwarn 1 but still, it's giving error. It may
be some silly mistake please let me know.


On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:

>
>
> On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:
> > Thank You Sir!
> >
> > Attached file can be downloaded from following link.
> >
> > https://fil.email/OR7Nsh0f
> > <https://fil.email/OR7Nsh0f?&showconfirmation=true>
> > 
> > Error
> >
> > ERROR 1 [file unk.itp, line 497]:
> >Duplicate atom index (23) in virtual_sites3
> > ___
> >
> > It support lone pair construction for halogens only. Please suggest some
> > alternatives.
>
> The link I provided before describes what you need to do. Please consult
> that information.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>


-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  
<http://www.linkedin.com/in/navneet-kumar-74391814a/>
<http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

Thank You Sir!

Attached file can be downloaded from following link.

https://fil.email/OR7Nsh0f
<https://fil.email/OR7Nsh0f?&showconfirmation=true>

Error

ERROR 1 [file unk.itp, line 497]:
  Duplicate atom index (23) in virtual_sites3
___

It support lone pair construction for halogens only. Please suggest some
alternatives.

On Sun, Aug 25, 2019 at 8:11 PM Justin Lemkul  wrote:

>
>
> On 8/25/19 8:33 AM, Navneet Kumar Singh wrote:
> > can you please help in solving this error while running MD simulation of
> > protein-ligand complex using CHARMM36 force field on GROMACS engine.
> >
> >
> >
> > *Command*
> >
> > *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr*
> >
> >
> > *ERROR*
> >
> >
> > *ERROR 1 [file unk.itp, line 497]:  Duplicate atom index (23) in
> > virtual_sites3*
> >
> >
> >
> **
> >
> > *unk.itp file indicated error/ Please find the attached file for more
> > details.*
>
> The mailing list does not accept attachments.
>
> Please see the information at
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs which
> specifically addresses this lone pair issue and how to deal with it.
> GROMACS does not easily support the kinds of lone pair/vsite
> construction that CHARMM requires for this kind of interaction.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>


-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  
<http://www.linkedin.com/in/navneet-kumar-74391814a/>
<http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] (no subject)

[Navneet Kumar Singh]

can you please help in solving this error while running MD simulation of
protein-ligand complex using CHARMM36 force field on GROMACS engine.



*Command*

*gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr*


*ERROR*


*ERROR 1 [file unk.itp, line 497]:  Duplicate atom index (23) in
virtual_sites3*


**

*unk.itp file indicated error/ Please find the attached file for more
details.*


















*   192223 1 9   19222321 9   512223 1
9   51222321 9[ virtual_sites3 ]; Site   from funct a   d   52
12323 2 0   -0.164[ exclusions ]; ai  aj152 1
 5223 1   5221 1   5222 1   5218 1   5219 1   5251
1   5250 1*


*___*

*CGenFF Server was used to prepare the toplogy and other required files for
th e small molecules*



-- 






-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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