Re: [gmx-users] gmx convert-tpr problem

[Gregory Man Kai Poon]

Hi Mark,

To clarify, I should be calling mdrun like:

gmx mdrun -s new.tpr -cpi old.cpt -deffnm old

?

I apologize ahead if this sounds obvious.

Kind regards,
Gregory

G

et Outlook for Android


From: Mark Abraham
Sent: Wednesday, April 5, 19:25
Subject: Re: [gmx-users] gmx convert-tpr problem
To: Discussion list for GROMACS users

Hi, As the messages suggest, if you would like to change the output names, you 
can't append. If you would like to append, don't change the output names. The 
old output files are there, but you've told mdrun to expect them to have 
different names, and to append to them, but used a checkpoint file that has 
different names. It doesn't know whether the error was in you using the wrong 
checkpoint file, or a mismatching output name, or that there are missing files, 
or that you don't want appending. Mark On Thu, 6 Apr 2017 00:43 Gregory Man Kai 
Poon wrote: > Hello all: > > > I am having problems extending my runs using 
convert-tpr in GROMACS > 2016.1. In the latest instance, for example, I have a 
100-ns run that I > want to extend to 200 ns. I used the convert-tpr command to 
get my new > .tpr file: > > > gmx convert-tpr -s md_0_100.tpr -until 200 -o 
md_100_200.tpr > > > With the new .tpr file in hand, I start mdrun: > > > gmx 
mdrun -s md_100_200.tpr -cpi md_0_100.cpt -v -deffnm 
 md_0_200 > > > At this point I get this error: > > > GROMACS: gmx mdrun, 
version 2016.1 > Executable: /usr/local/gromacs/bin/gmx > Data prefix: 
/usr/local/gromacs > Working dir: /media/i5/EXTREME 64/AGC_GTG2 > Command line: 
> gmx mdrun -s md_100_200.tpr -cpi md_0_100.cpt -v -deffnm md_100_200 > > 
Output file appending has been requested, > but some output files listed in the 
checkpoint file md_0_100.cpt > are not present or not named as the output files 
by the current program: > Expect output files present: > > Expected output 
files not present or named differently: > md_0_100.log > md_0_100.xtc > 
md_0_100.trr > md_0_100.edr > > 
--- > Program: gmx mdrun, 
version 2016.1 > Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 
177) > > Fatal error: > File appending requested, but 4 of the 4 output files 
are not present or > are > named differently. For safety reasons, GROMACS-2016 
and later only allows > file > appendi
 ng to be used when all files have the same names as they had in the > original 
run. Checkpointing is merely intended for plain continuation of > runs. > For 
safety reasons you must specify all file names (e.g. with -deffnm), and > all 
these files must match the names used in the run prior to checkpointing > since 
we will append to them by default. If the files are not available, > you > can 
add the -noappend flag to mdrun and write separate new parts. For mere > 
concatenation of files, you should use the gmx trjcat tool instead. > > For 
more information and tips for troubleshooting, please check the GROMACS > 
website at 
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FErrors=02%7C01%7Cgpoon%40gsu.edu%7Ccd5f1661e0be4bfea85608d47c7b0a58%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636270315275689367=wud%2BY7HyhMxHQhwPzSzJ836fq8vKy%2FUj9BjZ0EMscBY%3D=0
 > --- 
 > > > I checked, double-checked, triple-checked that all the files the error 
 > > > is > referring to is in the working directory. In fact, all the files 
 > > > (the > md_0_100.* files from the previous run) as well as md_100_200.tpr 
 > > > are in > the same folder (the working directory), in which the mdrun 
 > > > command is > invoked. Any suggestions would be appreciated. > > > Kind 
 > > > regards, > > Gregory > > -- > Gromacs Users mailing list > > * Please 
 > > > search the archive at > 
 > > > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List=02%7C01%7Cgpoon%40gsu.edu%7Ccd5f1661e0be4bfea85608d47c7b0a58%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636270315275689367=DpOZWBaO5Sr6Jt5JLKNXIU6Vj4AIrM%2Ba61T4OKeyvO8%3D=0
 > > >  before > posting! > > * Can't post? Read 
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15ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636270315275689367=tuv6gpyzuXApwVSv1rXZ1q8wxvruSmZhgjFnIq9zeks%3D=0
 > > * For (un)subscribe requests visit > 
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 or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing 
list * Please search the archive at 

Re: [gmx-users] gmx convert-tpr problem

[Mark Abraham]

Hi,

As the messages suggest, if you would like to change the output names, you
can't append. If you would like to append, don't change the output names.

The old output files are there, but you've told mdrun to expect them to
have different names, and to append to them, but used a checkpoint file
that has different names. It doesn't know whether the error was in you
using the wrong checkpoint file, or a mismatching output name, or that
there are missing files, or that you don't want appending.

Mark

On Thu, 6 Apr 2017 00:43 Gregory Man Kai Poon  wrote:

> Hello all:
>
>
> I am having problems extending my runs using convert-tpr in GROMACS
> 2016.1.  In the latest instance, for example, I have a 100-ns run that I
> want to extend to 200 ns.  I used the convert-tpr command to get my new
> .tpr file:
>
>
> gmx convert-tpr -s md_0_100.tpr -until 200 -o md_100_200.tpr
>
>
> With the new .tpr file in hand, I start mdrun:
>
>
> gmx mdrun -s md_100_200.tpr -cpi md_0_100.cpt -v -deffnm md_0_200
>
>
> At this point I get this error:
>
>
> GROMACS:  gmx mdrun, version 2016.1
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Working dir:  /media/i5/EXTREME 64/AGC_GTG2
> Command line:
>   gmx mdrun -s md_100_200.tpr -cpi md_0_100.cpt -v -deffnm md_100_200
>
> Output file appending has been requested,
> but some output files listed in the checkpoint file md_0_100.cpt
> are not present or not named as the output files by the current program:
> Expect output files present:
>
> Expected output files not present or named differently:
>   md_0_100.log
>   md_0_100.xtc
>   md_0_100.trr
>   md_0_100.edr
>
> ---
> Program: gmx mdrun, version 2016.1
> Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)
>
> Fatal error:
> File appending requested, but 4 of the 4 output files are not present or
> are
> named differently. For safety reasons, GROMACS-2016 and later only allows
> file
> appending to be used when all files have the same names as they had in the
> original run. Checkpointing is merely intended for plain continuation of
> runs.
> For safety reasons you must specify all file names (e.g. with -deffnm), and
> all these files must match the names used in the run prior to checkpointing
> since we will append to them by default. If the files are not available,
> you
> can add the -noappend flag to mdrun and write separate new parts. For mere
> concatenation of files, you should use the gmx trjcat tool instead.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
>
> I checked, double-checked, triple-checked that all the files the error is
> referring to is in the working directory.  In fact, all the files (the
> md_0_100.* files from the previous run) as well as md_100_200.tpr are in
> the same folder (the working directory), in which the mdrun command is
> invoked.  Any suggestions would be appreciated.
>
>
> Kind regards,
>
> Gregory
>
> --
> 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.
>
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Re: [gmx-users] gmx convert-tpr problem

[Justin Lemkul]

On 4/5/17 6:43 PM, Gregory Man Kai Poon wrote:

Hello all:


I am having problems extending my runs using convert-tpr in GROMACS 2016.1.  In 
the latest instance, for example, I have a 100-ns run that I want to extend to 
200 ns.  I used the convert-tpr command to get my new .tpr file:


gmx convert-tpr -s md_0_100.tpr -until 200 -o md_100_200.tpr


With the new .tpr file in hand, I start mdrun:


gmx mdrun -s md_100_200.tpr -cpi md_0_100.cpt -v -deffnm md_0_200


At this point I get this error:


GROMACS:  gmx mdrun, version 2016.1
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /media/i5/EXTREME 64/AGC_GTG2
Command line:
  gmx mdrun -s md_100_200.tpr -cpi md_0_100.cpt -v -deffnm md_100_200

Output file appending has been requested,
but some output files listed in the checkpoint file md_0_100.cpt
are not present or not named as the output files by the current program:
Expect output files present:

Expected output files not present or named differently:
  md_0_100.log
  md_0_100.xtc
  md_0_100.trr
  md_0_100.edr

---
Program: gmx mdrun, version 2016.1
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)

Fatal error:
File appending requested, but 4 of the 4 output files are not present or are
named differently. For safety reasons, GROMACS-2016 and later only allows file
appending to be used when all files have the same names as they had in the
original run. Checkpointing is merely intended for plain continuation of runs.
For safety reasons you must specify all file names (e.g. with -deffnm), and
all these files must match the names used in the run prior to checkpointing
since we will append to them by default. If the files are not available, you
can add the -noappend flag to mdrun and write separate new parts. For mere
concatenation of files, you should use the gmx trjcat tool instead.

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


I checked, double-checked, triple-checked that all the files the error is 
referring to is in the working directory.  In fact, all the files (the 
md_0_100.* files from the previous run) as well as md_100_200.tpr are in the 
same folder (the working directory), in which the mdrun command is invoked.  
Any suggestions would be appreciated.



The error message could probably use a bit of re-wording, but what mdrun is 
telling you is that the .cpt file tells mdrun that there should be md_0_100.* 
that are being written, but your use of -deffnm md_100_200 means the output 
files will be named md_100_200.* and mdrun is trying to append to the existing 
files with different file names.  Use -noappend if you're changing the output 
file names.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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[gmx-users] gmx convert-tpr problem

[Gregory Man Kai Poon]

Hello all:


I am having problems extending my runs using convert-tpr in GROMACS 2016.1.  In 
the latest instance, for example, I have a 100-ns run that I want to extend to 
200 ns.  I used the convert-tpr command to get my new .tpr file:


gmx convert-tpr -s md_0_100.tpr -until 200 -o md_100_200.tpr


With the new .tpr file in hand, I start mdrun:


gmx mdrun -s md_100_200.tpr -cpi md_0_100.cpt -v -deffnm md_0_200


At this point I get this error:


GROMACS:  gmx mdrun, version 2016.1
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /media/i5/EXTREME 64/AGC_GTG2
Command line:
  gmx mdrun -s md_100_200.tpr -cpi md_0_100.cpt -v -deffnm md_100_200

Output file appending has been requested,
but some output files listed in the checkpoint file md_0_100.cpt
are not present or not named as the output files by the current program:
Expect output files present:

Expected output files not present or named differently:
  md_0_100.log
  md_0_100.xtc
  md_0_100.trr
  md_0_100.edr

---
Program: gmx mdrun, version 2016.1
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)

Fatal error:
File appending requested, but 4 of the 4 output files are not present or are
named differently. For safety reasons, GROMACS-2016 and later only allows file
appending to be used when all files have the same names as they had in the
original run. Checkpointing is merely intended for plain continuation of runs.
For safety reasons you must specify all file names (e.g. with -deffnm), and
all these files must match the names used in the run prior to checkpointing
since we will append to them by default. If the files are not available, you
can add the -noappend flag to mdrun and write separate new parts. For mere
concatenation of files, you should use the gmx trjcat tool instead.

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


I checked, double-checked, triple-checked that all the files the error is 
referring to is in the working directory.  In fact, all the files (the 
md_0_100.* files from the previous run) as well as md_100_200.tpr are in the 
same folder (the working directory), in which the mdrun command is invoked.  
Any suggestions would be appreciated.


Kind regards,

Gregory

-- 
Gromacs Users mailing list

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

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Re: [gmx-users] Force Fields Keeping sp3 Nitrogen Groups Planar?

[Phillip Rauscher]

I see, thanks for your help!

On Wed, Apr 5, 2017 at 9:27 AM, Mark Abraham 
wrote:

> Hi,
>
> The protonation state is a decision you make in setting up the topology
> (what pH am I modelling?). Having done so, you get whatever amine model the
> force field specifies, and I expect that no force field has such a planar
> amine, because none actually have the improper dihedral you suggest they
> do, for the reason you suggest. :-)
>
> Mark
>
> On Wed, Apr 5, 2017 at 4:10 PM Phillip Rauscher 
> wrote:
>
> > Thanks so much for the reply Mark!  For my own curiosity, is there a way
> > that people generally deal with neutral sp3 Nitogens?  They're chiral
> > centers on simulation time scales, but on macroscopic scales pyramidal
> > inversion eliminates that.
> >
> > On Wed, Apr 5, 2017 at 1:16 AM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Amide nitrogen atoms are trigonal planar because the group is planar.
> > > There's no free rotation about the n-c bond, and the lone pair forms a
> > > hybrid orbital with the carbonyl.
> > >
> > > Mark
> > >
> > > On Tue, 4 Apr 2017 18:05 Phillip Rauscher 
> > wrote:
> > >
> > > > It occurs to me that an example would be helpful.  Here is an excerpt
> > > from
> > > > the OPLS aminoacids.rtp file detailing alanine:
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > *[ ALA ] [ atoms ]  Nopls_238   -0.500 1 H
> opls_241
> > > > 0.300 1 CAopls_224B   0.140 1 HAopls_140
> > > > 0.060 1 CBopls_135   -0.180 2HB1opls_140
> > > > 0.060 2HB2opls_1400.060 2HB3opls_140
> > > > 0.060 2  Copls_2350.500 3 Oopls_236
> > > > -0.500 3 [ bonds ] N H NCACAHACA
> CB
> > > > CA CCB   HB1CB   HB2CB   HB3 C O-C N
> [
> > > > impropers ]-CCA N Himproper_Z_N_X_Y CA+N
> > > > C Oimproper_O_C_X_Y *
> > > >
> > > > We can see that the Nitrogen is bound to atoms H, CA, and -C (on the
> > > > previous residue).  In the [impropers] section, an improper dihedral
> is
> > > > defined for these four atoms (with the nitrogen in both of the
> dihedral
> > > > planes).  If we look at the definition of that improper in the OPLS
> > > > ffbonded.itp file, we see the following:
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > *[ dihedraltypes ]; Improper OPLS dihedrals to keep groups planar.;
> > (OPLS
> > > > doesnt use impropers for chiral atoms).; Since these functions are
> > > periodic
> > > > of the form 1-cos(2*x), they are actually; implemented as proper
> > > dihedrals
> > > > [1+cos(2*x+180)] for the moment, ; to keep things compatible.; The
> > > defines
> > > > are used in ffoplsaa.rtp or directly in your .top file; Z -N?-X
> -Y
> > > > improper torsion#define improper_Z_N_X_Y180.0  4.18400
>  2*
> > > > Given the functional form and the parameters used, this potential has
> > > > minima at 0 and 180 degrees, thus keeping all four atoms (centered at
> > the
> > > > nitrogen) in the same plane.
> > > >
> > > > On Tue, Apr 4, 2017 at 10:38 AM, Phillip Rauscher <
> > > pmrausc...@uchicago.edu
> > > > >
> > > > wrote:
> > > >
> > > > > Hello all,
> > > > >
> > > > > I've noticed that in some of the force fields (in the aminoacid.rtp
> > > > > files), an improper dihedral is applied to the nitrogens in the
> > peptide
> > > > > bond (and sometimes other amine groups as well), which are all sp3
> > > > > hybridized with one lone pair.  Interestingly, the dihedral
> potential
> > > > > parameters serve to keep the groups trigonal planar, rather than
> > > > > tetrahedral.  More specifically, I've seen this in OPLS, Amber03,
> and
> > > > > Charmm27 - enough to indicate that it's not a mistake (besides the
> > fact
> > > > > that it's applied to ALL amino acids!)  The functional form of the
> > > > improper
> > > > > potential varies between force fields, but the lowest energy angle
> is
> > > > > always 0 or 180 indicating planar structure.
> > > > >
> > > > > Why is this done?  I've done some digging through the GROMACS
> > > > publications
> > > > > as well as those for the force fields and can't seem to find any
> > > > reference
> > > > > to this practice?  Is it an attempt to "average out" nitrogen
> > > inversions?
> > > > > Is it just to eliminate a chiral center?
> > > > >
> > > > > Thanks for your help!
> > > > >
> > > > > -Phil Rauscher
> > > > >
> > > > > --
> > > > > Phil Rauscher
> > > > > Graduate Student
> > > > > de Pablo and Rowan Research Groups
> > > > > Institute for Molecular Engineering
> > > > > University of Chicago
> > > 

Re: [gmx-users] Force Fields Keeping sp3 Nitrogen Groups Planar?

[Mark Abraham]

Hi,

The protonation state is a decision you make in setting up the topology
(what pH am I modelling?). Having done so, you get whatever amine model the
force field specifies, and I expect that no force field has such a planar
amine, because none actually have the improper dihedral you suggest they
do, for the reason you suggest. :-)

Mark

On Wed, Apr 5, 2017 at 4:10 PM Phillip Rauscher 
wrote:

> Thanks so much for the reply Mark!  For my own curiosity, is there a way
> that people generally deal with neutral sp3 Nitogens?  They're chiral
> centers on simulation time scales, but on macroscopic scales pyramidal
> inversion eliminates that.
>
> On Wed, Apr 5, 2017 at 1:16 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Amide nitrogen atoms are trigonal planar because the group is planar.
> > There's no free rotation about the n-c bond, and the lone pair forms a
> > hybrid orbital with the carbonyl.
> >
> > Mark
> >
> > On Tue, 4 Apr 2017 18:05 Phillip Rauscher 
> wrote:
> >
> > > It occurs to me that an example would be helpful.  Here is an excerpt
> > from
> > > the OPLS aminoacids.rtp file detailing alanine:
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > *[ ALA ] [ atoms ]  Nopls_238   -0.500 1 Hopls_241
> > > 0.300 1 CAopls_224B   0.140 1 HAopls_140
> > > 0.060 1 CBopls_135   -0.180 2HB1opls_140
> > > 0.060 2HB2opls_1400.060 2HB3opls_140
> > > 0.060 2  Copls_2350.500 3 Oopls_236
> > > -0.500 3 [ bonds ] N H NCACAHACACB
> > > CA CCB   HB1CB   HB2CB   HB3 C O-C N [
> > > impropers ]-CCA N Himproper_Z_N_X_Y CA+N
> > > C Oimproper_O_C_X_Y *
> > >
> > > We can see that the Nitrogen is bound to atoms H, CA, and -C (on the
> > > previous residue).  In the [impropers] section, an improper dihedral is
> > > defined for these four atoms (with the nitrogen in both of the dihedral
> > > planes).  If we look at the definition of that improper in the OPLS
> > > ffbonded.itp file, we see the following:
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > *[ dihedraltypes ]; Improper OPLS dihedrals to keep groups planar.;
> (OPLS
> > > doesnt use impropers for chiral atoms).; Since these functions are
> > periodic
> > > of the form 1-cos(2*x), they are actually; implemented as proper
> > dihedrals
> > > [1+cos(2*x+180)] for the moment, ; to keep things compatible.; The
> > defines
> > > are used in ffoplsaa.rtp or directly in your .top file; Z -N?-X -Y
> > > improper torsion#define improper_Z_N_X_Y180.0  4.18400   2*
> > > Given the functional form and the parameters used, this potential has
> > > minima at 0 and 180 degrees, thus keeping all four atoms (centered at
> the
> > > nitrogen) in the same plane.
> > >
> > > On Tue, Apr 4, 2017 at 10:38 AM, Phillip Rauscher <
> > pmrausc...@uchicago.edu
> > > >
> > > wrote:
> > >
> > > > Hello all,
> > > >
> > > > I've noticed that in some of the force fields (in the aminoacid.rtp
> > > > files), an improper dihedral is applied to the nitrogens in the
> peptide
> > > > bond (and sometimes other amine groups as well), which are all sp3
> > > > hybridized with one lone pair.  Interestingly, the dihedral potential
> > > > parameters serve to keep the groups trigonal planar, rather than
> > > > tetrahedral.  More specifically, I've seen this in OPLS, Amber03, and
> > > > Charmm27 - enough to indicate that it's not a mistake (besides the
> fact
> > > > that it's applied to ALL amino acids!)  The functional form of the
> > > improper
> > > > potential varies between force fields, but the lowest energy angle is
> > > > always 0 or 180 indicating planar structure.
> > > >
> > > > Why is this done?  I've done some digging through the GROMACS
> > > publications
> > > > as well as those for the force fields and can't seem to find any
> > > reference
> > > > to this practice?  Is it an attempt to "average out" nitrogen
> > inversions?
> > > > Is it just to eliminate a chiral center?
> > > >
> > > > Thanks for your help!
> > > >
> > > > -Phil Rauscher
> > > >
> > > > --
> > > > Phil Rauscher
> > > > Graduate Student
> > > > de Pablo and Rowan Research Groups
> > > > Institute for Molecular Engineering
> > > > University of Chicago
> > > >
> > >
> > >
> > >
> > > --
> > > Phil Rauscher
> > > Graduate Student
> > > de Pablo and Rowan Research Groups
> > > Institute for Molecular Engineering
> > > University of Chicago
> > > --
> > > 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 

Re: [gmx-users] Force Fields Keeping sp3 Nitrogen Groups Planar?

[Phillip Rauscher]

Thanks so much for the reply Mark!  For my own curiosity, is there a way
that people generally deal with neutral sp3 Nitogens?  They're chiral
centers on simulation time scales, but on macroscopic scales pyramidal
inversion eliminates that.

On Wed, Apr 5, 2017 at 1:16 AM, Mark Abraham 
wrote:

> Hi,
>
> Amide nitrogen atoms are trigonal planar because the group is planar.
> There's no free rotation about the n-c bond, and the lone pair forms a
> hybrid orbital with the carbonyl.
>
> Mark
>
> On Tue, 4 Apr 2017 18:05 Phillip Rauscher  wrote:
>
> > It occurs to me that an example would be helpful.  Here is an excerpt
> from
> > the OPLS aminoacids.rtp file detailing alanine:
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *[ ALA ] [ atoms ]  Nopls_238   -0.500 1 Hopls_241
> > 0.300 1 CAopls_224B   0.140 1 HAopls_140
> > 0.060 1 CBopls_135   -0.180 2HB1opls_140
> > 0.060 2HB2opls_1400.060 2HB3opls_140
> > 0.060 2  Copls_2350.500 3 Oopls_236
> > -0.500 3 [ bonds ] N H NCACAHACACB
> > CA CCB   HB1CB   HB2CB   HB3 C O-C N [
> > impropers ]-CCA N Himproper_Z_N_X_Y CA+N
> > C Oimproper_O_C_X_Y *
> >
> > We can see that the Nitrogen is bound to atoms H, CA, and -C (on the
> > previous residue).  In the [impropers] section, an improper dihedral is
> > defined for these four atoms (with the nitrogen in both of the dihedral
> > planes).  If we look at the definition of that improper in the OPLS
> > ffbonded.itp file, we see the following:
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *[ dihedraltypes ]; Improper OPLS dihedrals to keep groups planar.; (OPLS
> > doesnt use impropers for chiral atoms).; Since these functions are
> periodic
> > of the form 1-cos(2*x), they are actually; implemented as proper
> dihedrals
> > [1+cos(2*x+180)] for the moment, ; to keep things compatible.; The
> defines
> > are used in ffoplsaa.rtp or directly in your .top file; Z -N?-X -Y
> > improper torsion#define improper_Z_N_X_Y180.0  4.18400   2*
> > Given the functional form and the parameters used, this potential has
> > minima at 0 and 180 degrees, thus keeping all four atoms (centered at the
> > nitrogen) in the same plane.
> >
> > On Tue, Apr 4, 2017 at 10:38 AM, Phillip Rauscher <
> pmrausc...@uchicago.edu
> > >
> > wrote:
> >
> > > Hello all,
> > >
> > > I've noticed that in some of the force fields (in the aminoacid.rtp
> > > files), an improper dihedral is applied to the nitrogens in the peptide
> > > bond (and sometimes other amine groups as well), which are all sp3
> > > hybridized with one lone pair.  Interestingly, the dihedral potential
> > > parameters serve to keep the groups trigonal planar, rather than
> > > tetrahedral.  More specifically, I've seen this in OPLS, Amber03, and
> > > Charmm27 - enough to indicate that it's not a mistake (besides the fact
> > > that it's applied to ALL amino acids!)  The functional form of the
> > improper
> > > potential varies between force fields, but the lowest energy angle is
> > > always 0 or 180 indicating planar structure.
> > >
> > > Why is this done?  I've done some digging through the GROMACS
> > publications
> > > as well as those for the force fields and can't seem to find any
> > reference
> > > to this practice?  Is it an attempt to "average out" nitrogen
> inversions?
> > > Is it just to eliminate a chiral center?
> > >
> > > Thanks for your help!
> > >
> > > -Phil Rauscher
> > >
> > > --
> > > Phil Rauscher
> > > Graduate Student
> > > de Pablo and Rowan Research Groups
> > > Institute for Molecular Engineering
> > > University of Chicago
> > >
> >
> >
> >
> > --
> > Phil Rauscher
> > Graduate Student
> > de Pablo and Rowan Research Groups
> > Institute for Molecular Engineering
> > University of Chicago
> > --
> > 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
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>



-- 
Phil Rauscher
Graduate Student
de Pablo and Rowan Research Groups
Institute for Molecular Engineering
University of Chicago
-- 
Gromacs 

Re: [gmx-users] how to know solvent molecule number

[Vytautas Rakeviius]

Oh sorry number of atoms you will have to divide by number of atoms in 
ethanolamine. 

On Wednesday, April 5, 2017 4:45 PM, Vytautas Rakeviius 
 wrote:
 

 head -n 2 obj.gro | tail -n 1Print number of molecules in obj.gro file. 
Solvate then do same on new file:
head -n 2 obj_solv.gro | tail -n 1All you need is difference.
 

On Wednesday, April 5, 2017 4:13 PM, Chintan Bhagat  
wrote:
 

 Hello,

I want to do stimulation of my protein in solvent, ethanolamine (different
percentage).
I have made box of 1 nm and then using command
"gmx solvate -cp 1AKI_newbox.gro -cs ethanolamine.gro -o 1AKI_solv.gro -p
topol.top",
As per my knowledge, i solvated my protein in ethanolamine.
Now I want to know the number of ethanolamine molecule present in box. Then
I looked in to *.top* file but no information is availble in the file (SOL).
(As per intruction, program is only hard-coded to update the topology in
the case of water).
I found increase in number of molecules from 7200 to 128004 in
/home/lab1/Desktop/md2/1AKI_processed.gro.gro and 1AKI_solv.gro,
respectively. It means something is inserted in box (must be
ethanolamine!-my guess)
How can i know number of ethanolamine molecules?


for reference please find attched files.

Thanking you in advance.
-- 
Regards,
Chintan Bhagat
Research scholar,
Veer Narmad South Gujarat University,
India
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Re: [gmx-users] how to know solvent molecule number

[Vytautas Rakeviius]

head -n 2 obj.gro | tail -n 1Print number of molecules in obj.gro file. Solvate 
then do same on new file:
head -n 2 obj_solv.gro | tail -n 1All you need is difference.
 

On Wednesday, April 5, 2017 4:13 PM, Chintan Bhagat  
wrote:
 

 Hello,

I want to do stimulation of my protein in solvent, ethanolamine (different
percentage).
I have made box of 1 nm and then using command
"gmx solvate -cp 1AKI_newbox.gro -cs ethanolamine.gro -o 1AKI_solv.gro -p
topol.top",
As per my knowledge, i solvated my protein in ethanolamine.
Now I want to know the number of ethanolamine molecule present in box. Then
I looked in to *.top* file but no information is availble in the file (SOL).
(As per intruction, program is only hard-coded to update the topology in
the case of water).
I found increase in number of molecules from 7200 to 128004 in
/home/lab1/Desktop/md2/1AKI_processed.gro.gro and 1AKI_solv.gro,
respectively. It means something is inserted in box (must be
ethanolamine!-my guess)
How can i know number of ethanolamine molecules?


for reference please find attched files.

Thanking you in advance.
-- 
Regards,
Chintan Bhagat
Research scholar,
Veer Narmad South Gujarat University,
India
-- 
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Re: [gmx-users] how to know solvent molecule number

[spss4]

 - Message from Chintan Bhagat  -
    Date: Wed, 5 Apr 2017 18:42:30 +0530
    From: Chintan Bhagat 
Reply-To: gmx-us...@gromacs.org
Subject: [gmx-users] how to know solvent molecule number
      To: gromacs.org_gmx-users@maillist.sys.kth.se


Hello,

I want to do stimulation of my protein in solvent, ethanolamine

(different

percentage).
I have made box of 1 nm and then using command
"gmx solvate -cp 1AKI_newbox.gro -cs ethanolamine.gro -o 1AKI_solv.gro -p
topol.top",
As per my knowledge, i solvated my protein in ethanolamine.
Now I want to know the number of ethanolamine molecule present in box.
Then
I looked in to *.top* file but no information is availble in the file
(SOL).
(As per intruction, program is only hard-coded to update the topology in
the case of water).
I found increase in number of molecules from 7200 to 128004 in
/home/lab1/Desktop/md2/1AKI_processed.gro.gro and 1AKI_solv.gro,
respectively. It means something is inserted in box (must be
ethanolamine!-my guess)
How can i know number of ethanolamine molecules?

for reference please find attched files.

Thanking you in advance.
--
Regards,
Chintan Bhagat
Research scholar,
Veer Narmad South Gujarat University,India


Hii
I think you are doing some mistakes. 1AKI_processed.gro should contain 129
molecules and 1960 atoms as you are using 1AKI.pdb (your file contains SOL
also??). If you want to add a certain number of solvent then you can use
-cs -maxsol   command. If you want to add solvent randomly using -cs then
you can get number of solvents from 1AKI_sol.gro file and write the number
in topol.top file..

- End message from Chintan Bhagat  -
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Re: [gmx-users] how to know solvent molecule number

[Mark Abraham]

Hi,

gmx solvate reports on the terminal what it has done, doesn't it? Someone
needs to update the topology, so we wouldn't suppress the number you need
;-)

Mark

On Wed, Apr 5, 2017 at 3:13 PM Chintan Bhagat  wrote:

> Hello,
>
> I want to do stimulation of my protein in solvent, ethanolamine (different
> percentage).
> I have made box of 1 nm and then using command
> "gmx solvate -cp 1AKI_newbox.gro -cs ethanolamine.gro -o 1AKI_solv.gro -p
> topol.top",
> As per my knowledge, i solvated my protein in ethanolamine.
> Now I want to know the number of ethanolamine molecule present in box. Then
> I looked in to *.top* file but no information is availble in the file
> (SOL).
> (As per intruction, program is only hard-coded to update the topology in
> the case of water).
> I found increase in number of molecules from 7200 to 128004 in
> /home/lab1/Desktop/md2/1AKI_processed.gro.gro and 1AKI_solv.gro,
> respectively. It means something is inserted in box (must be
> ethanolamine!-my guess)
> How can i know number of ethanolamine molecules?
>
>
> for reference please find attched files.
>
> Thanking you in advance.
> --
> Regards,
> Chintan Bhagat
> Research scholar,
> Veer Narmad South Gujarat University,
> India
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] how to know solvent molecule number

[Justin Lemkul]

On 4/5/17 9:12 AM, Chintan Bhagat wrote:

Hello,

I want to do stimulation of my protein in solvent, ethanolamine (different
percentage).
I have made box of 1 nm and then using command
"gmx solvate -cp 1AKI_newbox.gro -cs ethanolamine.gro -o 1AKI_solv.gro -p
topol.top",
As per my knowledge, i solvated my protein in ethanolamine.
Now I want to know the number of ethanolamine molecule present in box. Then
I looked in to *.top* file but no information is availble in the file (SOL).
(As per intruction, program is only hard-coded to update the topology in
the case of water).
I found increase in number of molecules from 7200 to 128004 in
/home/lab1/Desktop/md2/1AKI_processed.gro.gro and 1AKI_solv.gro,
respectively. It means something is inserted in box (must be
ethanolamine!-my guess)
How can i know number of ethanolamine molecules?



Use grep -c with a unique atom name to count the number of any given molecule in 
the system.




for reference please find attched files.



The mailing list does not accept attachments.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Regarding viewing Trajectories

[Mark Abraham]

Hi,

On Wed, Apr 5, 2017 at 3:26 PM Dilip H N  wrote:

> Thamk you ,
> But in my RDF i have got a peaks(solvation shells) with Carbon of amino
> acid with ammonia in ammonia-water mixture,


I don't understand how an ammonia-water mixture has amino-acid carbons in
it. Please describe your system and RDF accurately the first time.

so i need to analyse why that
> peak has been formed, which can be viewed by visualizing the trajectories
>  in vmd.
> So i need to see that at what time frame/step has the bond
> formed/particular molecule is closer to the preferred atom, since with this
> i can give justification to my results...
>

"Justify" doesn't seem like the right word. You can add a physical
interpretation to what you've computed, once you're sure you've computed
the thing you want. But doing so only makes sense if it relates to the aim
of your study, which is kind of your business to already know before you
start computing things. :-)

So how can i view those molecules that have been more closer/bond formation
> with specific molecule has occurred...since viewing the whole trajectory
> time frame (i have 6002 frames) is time consuming...
> I wrote in Graphical representation > selected atoms > all within 5 of
> protein and i am viewing it for every time frame...
>

Then either every frame contributes (e.g. you have lots of carbon atoms and
lots of ammonia and a lot of the RDF is in that first peak, so there is a
very low chance that any frame has zero carbon atoms close to any ammonia
atom), or you haven't been specific enough in describing to VMD what you
actually want.

Mark


>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
>
> On Wed, Apr 5, 2017 at 12:07 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > A peak in a distance distribution function by definition is contributed
> to
> > by lots of molecules around that distance from lots of different central
> > points. There's no single frame for each point.
> >
> > If you look at a normal histogram, and see a peak, asking "which single
> > data point made this" is not meaningful, because multiple data points
> have
> > normally contributed.
> >
> > Mark
> >
> > On Wed, Apr 5, 2017 at 6:40 AM Dilip H N 
> > wrote:
> >
> > > Hello.,
> > > In RDF of amino acid with ammonia and water mixture, i have got a 1st
> > peak,
> > > 2nd peak (solvation shell), and i need to view this in the vmd by
> making
> > > use of the trajectories (trr/xtc files), so while viewing the
> > trajectories
> > >
> > > 1] how can i view that exact trajectory at which i have got the
> > particular
> > > peak in RDF (since that would mean either H-bond formation/probability
> of
> > > tht molecule close to that)
> > > because viewing each frame to find it would take literally lot of time,
> > ...
> > >
> > > Thank you.
> > >
> > > --
> > > With Best Regards,
> > >
> > > DILIP.H.N
> > > Ph.D Student
> > >
> > >
> > >
> > >    Sent with Mailtrack
> > > <
> > > https://mailtrack.io/install?source=signature=en;
> > referral=cy16f01.di...@nitk.edu.in=22
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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> >
> > * Please search the archive at http://www.gromacs.org/
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
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> Gromacs Users mailing list
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Re: [gmx-users] Regarding viewing Trajectories

[Dilip H N]

Thamk you ,
But in my RDF i have got a peaks(solvation shells) with Carbon of amino
acid with ammonia in ammonia-water mixture, so i need to analyse why that
peak has been formed, which can be viewed by visualizing the trajectories
 in vmd.
So i need to see that at what time frame/step has the bond
formed/particular molecule is closer to the preferred atom, since with this
i can give justification to my results...
So how can i view those molecules that have been more closer/bond formation
with specific molecule has occurred...since viewing the whole trajectory
time frame (i have 6002 frames) is time consuming...
I wrote in Graphical representation > selected atoms > all within 5 of
protein and i am viewing it for every time frame...



   Sent with Mailtrack


On Wed, Apr 5, 2017 at 12:07 PM, Mark Abraham 
wrote:

> Hi,
>
> A peak in a distance distribution function by definition is contributed to
> by lots of molecules around that distance from lots of different central
> points. There's no single frame for each point.
>
> If you look at a normal histogram, and see a peak, asking "which single
> data point made this" is not meaningful, because multiple data points have
> normally contributed.
>
> Mark
>
> On Wed, Apr 5, 2017 at 6:40 AM Dilip H N 
> wrote:
>
> > Hello.,
> > In RDF of amino acid with ammonia and water mixture, i have got a 1st
> peak,
> > 2nd peak (solvation shell), and i need to view this in the vmd by making
> > use of the trajectories (trr/xtc files), so while viewing the
> trajectories
> >
> > 1] how can i view that exact trajectory at which i have got the
> particular
> > peak in RDF (since that would mean either H-bond formation/probability of
> > tht molecule close to that)
> > because viewing each frame to find it would take literally lot of time,
> ...
> >
> > Thank you.
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> >
> >
> >
> >    Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature=en;
> referral=cy16f01.di...@nitk.edu.in=22
> > >
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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[gmx-users] how to know solvent molecule number

[Chintan Bhagat]

Hello,

I want to do stimulation of my protein in solvent, ethanolamine (different
percentage).
I have made box of 1 nm and then using command
"gmx solvate -cp 1AKI_newbox.gro -cs ethanolamine.gro -o 1AKI_solv.gro -p
topol.top",
As per my knowledge, i solvated my protein in ethanolamine.
Now I want to know the number of ethanolamine molecule present in box. Then
I looked in to *.top* file but no information is availble in the file (SOL).
(As per intruction, program is only hard-coded to update the topology in
the case of water).
I found increase in number of molecules from 7200 to 128004 in
/home/lab1/Desktop/md2/1AKI_processed.gro.gro and 1AKI_solv.gro,
respectively. It means something is inserted in box (must be
ethanolamine!-my guess)
How can i know number of ethanolamine molecules?


for reference please find attched files.

Thanking you in advance.
-- 
Regards,
Chintan Bhagat
Research scholar,
Veer Narmad South Gujarat University,
India
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Re: [gmx-users] gmx mdrun

[Vytautas Rakeviius]

"my CPU switches off automatically"? Can you expain what actually happens. 
Windows go to sleep etc?Also you should do such things on Linux, cygwin is not 
that fast as you see in warning message.
 

On Sunday, April 2, 2017 11:24 AM, Neha Gupta  
wrote:
 

 Hi gromacs users,


I am using Gromacs 5.1.1 in windows cygwin.

When I run long calculations my CPU switches off automatically (just before
writing the coordinate file .gro) . How to prevent this and ensure
longevity of CPU?

Running on 1 node with total 8 logical cores
Hardware detected:
  CPU info:
    Vendor: AuthenticAMD
    Brand:  AMD FX-8370E Eight-Core Processor
    Family: 21  model:  2  stepping:  0



I also observed these in log file


SIMD instructions most likely to fit this hardware: AVX_128_FMA
 SIMD instructions selected at GROMACS compile time: SSE4.1


Binary not matching hardware - you might be losing performance.
SIMD instructions most likely to fit this hardware: AVX_128_FMA
SIMD instructions selected at GROMACS compile time: SSE4.1


The current CPU can measure timings more accurately than the code in gmx
was configured to use. This might affect your simulation speed as accurate
timings are needed for load-balancing.
Please consider rebuilding gmx with the GMX_USE_RDTSCP=ON CMake option.



Thanks,
Neha
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Re: [gmx-users] determining restraints for pulling

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 4/5/17 8:04 AM, abhisek Mondal wrote:

Hello Justin,

Can you provide some direction to this approach I'm using for performing
umbrella sampling of a protein-ligand complex ?

I had restrained it during the equilibration of the molecule. As advised in the
Protein-ligand simulation tutorial. But I'm unsure regarding what kind of
treatment I'm supposed to give the complex while targeting for umbrella
sampling. Do I need to restrain the ligand during equilibration ?

I have solved the crystal structure of the complex and want to determine if I
pull out the ligand then how the side chains reorient according to the ligand
withdrawal. That's the goal.

Some suggestions regarding the issue will be highly appreciated.



What does your examination of the literature for similar systems suggest as an 
appropriate protocol?


-Justin


Thank you

On Wed, Apr 5, 2017 at 3:51 PM, abhisek Mondal > wrote:

I had restrained it during the equilibration of the molecule. As advised in
the Protein-ligand simulation tutorial. But I'm unsure regarding what kind
of treatment I'm supposed to give the complex while targeting for umbrella
sampling. Do I need to restrain the ligand during equilibration ?

I have solved the crystal structure of the complex and want to determine if
I pull out the ligand then how the side chains reorient according to the
ligand withdrawal. That's the goal.

On Wed, Apr 5, 2017 at 3:09 PM, Mark Abraham > wrote:

Hi,

Why are you trying to keep the ligand in place (by restraining it) and 
pull
it out?

Mark

On Wed, 5 Apr 2017 09:51 abhisek Mondal > wrote:

> Hi,
>
> I'm trying to pull a ligand from a protein-ligand complex. As per the
> ligand-protein tutorial, I have restrained the ligand in topology 
file and
> it looks like:
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include ligand topology
> #include "drg.itp"
>
> ; Include position restraints
> #ifdef POSRES_LIG
> #include "posre_ACO.itp"
> #endif
>
> ; Include water topology
> #include "gromos43a1.ff/spc.itp"
>
> In the md_pull.mdp, I'm using:
>
> title   = Umbrella pulling simulation
> define  = -DPOSRES
> ; Run parameters
> integrator  = md;applying leap frog algorithm
>
> So, is it proper for pulling ligand (ACO) from the protein or I'm 
doing
> something wrong ? I'm really lost here, please help me out.
>
> Thank you.
>
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
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 before
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--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/




--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of 

Re: [gmx-users] (no subject)

[Erik Marklund]

Dear Maria,

Are you confusing gromos and gromacs?

In the manual, under the Force fields heading: "GROMACS 2016 includes several 
force fields, and additional ones are available on the website. If you do not 
know which one to select we recommend GROMOS-96 for united-atom setups and 
OPLS-AA/L for all-atom parameters. That said, we describe the available options 
in some detail.”

(The comment about OPLS-AA/L is probably very old and in need of revision.)

Then follows subsections describing a range of supported force fields, most of 
which are all-atom. The phrase “united-atom” occurs only once in the manual, in 
the sentence quoted above. What made you think gromacs is united-atom only?

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 5 Apr 2017, at 12:00, maria khan 
> wrote:

Dear Erik..

I have studied the manuals of gromacs and from that i came to know that
gromacs use united atom ff thats why i asked and in manuals many things has
been explained by quantum basis,,which is not understandable for me.

How can i find ff parameters for my ligand of interest?? also if
ff parameters are not in published form then it means i will not be able to
use that ligand for MD run?? My ligand of interest is alkaloid. and i dont
know how can i make the parameters for it.

Thank you.
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Re: [gmx-users] Hydrogen bond occupancy

[Mark Abraham]

Hi,

On Wed, Apr 5, 2017 at 1:09 PM Neha Gupta  wrote:

> Hi,
>
> Thank you for the reply.
>
> However, I don't get the same bonds as obtained through docking.  Those
> hydrogen bonds have vanished, I presume during the simulation duration of
> 2ns.
>

Sounds like it. Visualizing your trajectory would be an obvious stage in
understanding what is happening. There's no particular reason to expect two
different approximate model physics to agree with each other, unless
they've been already shown to have good agreement.


> The bonding takes place with different protein residues. One donor -
> acceptor has higher percentage (29%)  and the other has very less
> percentage (0.05%)
>
> Can someone tell me what does it mean?
>

It means that one bond has a higher propensity to persist than another.
Only you can put that in context.

Mark


>
> Thanks,
> Neha
>
>
>
>
>
> On Wed, Apr 5, 2017 at 1:34 PM, Erik Marklund 
> wrote:
>
> > Dear Neha,
> >
> > What fraction of the time the ligand hydrogen bonds to whatever it
> > interacts with.
> >
> > Kind regards,
> > Erik
> > __
> > Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> > Department of Chemistry – BMC, Uppsala University
> > +46 (0)18 471 4539 <018-471%2045%2039>
> > erik.markl...@kemi.uu.se
> >
> > On 5 Apr 2017, at 10:00, Neha Gupta  nehaphysic...@gmail.com>> wrote:
> >
> > Hi gromacs users,
> >
> > What is meant by Hydrogen bond occupancy in protein ligand simulations?
> >
> > What information do we extract from % of hydrogen bond occupancy?
> >
> > Thanks,
> > Neha
> > --
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Re: [gmx-users] Hydrogen bond occupancy

[Neha Gupta]

Hi,

Thank you for the reply.

However, I don't get the same bonds as obtained through docking.  Those
hydrogen bonds have vanished, I presume during the simulation duration of
2ns.

The bonding takes place with different protein residues. One donor -
acceptor has higher percentage (29%)  and the other has very less
percentage (0.05%)

Can someone tell me what does it mean?

Thanks,
Neha





On Wed, Apr 5, 2017 at 1:34 PM, Erik Marklund 
wrote:

> Dear Neha,
>
> What fraction of the time the ligand hydrogen bonds to whatever it
> interacts with.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se
>
> On 5 Apr 2017, at 10:00, Neha Gupta > wrote:
>
> Hi gromacs users,
>
> What is meant by Hydrogen bond occupancy in protein ligand simulations?
>
> What information do we extract from % of hydrogen bond occupancy?
>
> Thanks,
> Neha
> --
> Gromacs Users mailing list
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Re: [gmx-users] determining restraints for pulling

[abhisek Mondal]

I had restrained it during the equilibration of the molecule. As advised in
the Protein-ligand simulation tutorial. But I'm unsure regarding what kind
of treatment I'm supposed to give the complex while targeting for umbrella
sampling. Do I need to restrain the ligand during equilibration ?

I have solved the crystal structure of the complex and want to determine if
I pull out the ligand then how the side chains reorient according to the
ligand withdrawal. That's the goal.

On Wed, Apr 5, 2017 at 3:09 PM, Mark Abraham 
wrote:

> Hi,
>
> Why are you trying to keep the ligand in place (by restraining it) and pull
> it out?
>
> Mark
>
> On Wed, 5 Apr 2017 09:51 abhisek Mondal  wrote:
>
> > Hi,
> >
> > I'm trying to pull a ligand from a protein-ligand complex. As per the
> > ligand-protein tutorial, I have restrained the ligand in topology file
> and
> > it looks like:
> >
> > ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre.itp"
> > #endif
> >
> > ; Include ligand topology
> > #include "drg.itp"
> >
> > ; Include position restraints
> > #ifdef POSRES_LIG
> > #include "posre_ACO.itp"
> > #endif
> >
> > ; Include water topology
> > #include "gromos43a1.ff/spc.itp"
> >
> > In the md_pull.mdp, I'm using:
> >
> > title   = Umbrella pulling simulation
> > define  = -DPOSRES
> > ; Run parameters
> > integrator  = md;applying leap frog algorithm
> >
> > So, is it proper for pulling ligand (ACO) from the protein or I'm doing
> > something wrong ? I'm really lost here, please help me out.
> >
> > Thank you.
> >
> >
> > --
> > Abhisek Mondal
> >
> > *Senior Research Fellow*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
> > *INDIA*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

On Wed, Apr 5, 2017 at 12:00 PM maria khan 
wrote:

> Dear Erik..
>
> I have studied the manuals of gromacs and from that i came to know that
> gromacs use united atom ff thats why i asked and in manuals many things has
>

All the MD packages *can* deploy united-atom force fields. To my knowledge,
none of them require or prohibit it. :-)


> been explained by quantum basis,,which is not understandable for me.
>
> How can i find ff parameters for my ligand of interest?? also if
> ff parameters are not in published form then it means i will not be able to
> use that ligand for MD run?? My ligand of interest is alkaloid. and i dont
> know how can i make the parameters for it.
>

There's introductory level guidance available here
http://www.gromacs.org/Documentation/How-tos/Parameterization but you are
warned there that this is not a topic suitable for a beginner. At the very
least, use one of the several different packages that provide automated
force-field-specific parameterization of e.g. ligand molecules, having
planned how you will assess the quality of the parameterization before
attempting to use it to solve a problem whose answer you do not know.

Mark


> Thank you.
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Re: [gmx-users] (no subject)

[Vytautas Rakeviius]

You can use acpype to prepare ligands for MD run.
 

On Wednesday, April 5, 2017 1:01 PM, maria khan 
 wrote:
 

 Dear Erik..

I have studied the manuals of gromacs and from that i came to know that
gromacs use united atom ff thats why i asked and in manuals many things has
been explained by quantum basis,,which is not understandable for me.

How can i find ff parameters for my ligand of interest?? also if
ff parameters are not in published form then it means i will not be able to
use that ligand for MD run?? My ligand of interest is alkaloid. and i dont
know how can i make the parameters for it.

Thank you.
-- 
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[gmx-users] (no subject)

[maria khan]

Dear Erik..

I have studied the manuals of gromacs and from that i came to know that
gromacs use united atom ff thats why i asked and in manuals many things has
been explained by quantum basis,,which is not understandable for me.

How can i find ff parameters for my ligand of interest?? also if
ff parameters are not in published form then it means i will not be able to
use that ligand for MD run?? My ligand of interest is alkaloid. and i dont
know how can i make the parameters for it.

Thank you.
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Re: [gmx-users] determining restraints for pulling

[Mark Abraham]

Hi,

Why are you trying to keep the ligand in place (by restraining it) and pull
it out?

Mark

On Wed, 5 Apr 2017 09:51 abhisek Mondal  wrote:

> Hi,
>
> I'm trying to pull a ligand from a protein-ligand complex. As per the
> ligand-protein tutorial, I have restrained the ligand in topology file and
> it looks like:
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include ligand topology
> #include "drg.itp"
>
> ; Include position restraints
> #ifdef POSRES_LIG
> #include "posre_ACO.itp"
> #endif
>
> ; Include water topology
> #include "gromos43a1.ff/spc.itp"
>
> In the md_pull.mdp, I'm using:
>
> title   = Umbrella pulling simulation
> define  = -DPOSRES
> ; Run parameters
> integrator  = md;applying leap frog algorithm
>
> So, is it proper for pulling ligand (ACO) from the protein or I'm doing
> something wrong ? I'm really lost here, please help me out.
>
> Thank you.
>
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
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Re: [gmx-users] Ligand simulation

[Mark Abraham]

Hi,

On Wed, 5 Apr 2017 08:49 RAHUL SURESH  wrote:

> for Command
>
>
>
> *gmx grompp -f em.mdp -c solv.gro -p conformer.top -o ions.tpr*
> I get the following error.
>
>
> *Warning: atom name 5839 in conformer.top and solv.gro does not match (H81
> - 1H8)Warning: atom name 5840 in conformer.top and solv.gro does not match
> (H82 - 2H8)*
>
> Is it really an issue or can I use -maxwarn?
>

Only you can know whether the difference in naming reflects your intent, or
not. Why did you generate the topology from a coordinate file that is
different from what you are using with grompp?

Mark

--
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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Re: [gmx-users] Hydrogen bond occupancy

[Erik Marklund]

Dear Neha,

What fraction of the time the ligand hydrogen bonds to whatever it interacts 
with.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 5 Apr 2017, at 10:00, Neha Gupta 
> wrote:

Hi gromacs users,

What is meant by Hydrogen bond occupancy in protein ligand simulations?

What information do we extract from % of hydrogen bond occupancy?

Thanks,
Neha
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Re: [gmx-users] Charmm ff compatibility with Gromacs

[Erik Marklund]

Dear Maria,

Please see below.

Kind regards,
Erik

> On 5 Apr 2017, at 09:08, maria khan  wrote:
> 
> Hello Gromacs users..
> 
> Charmm 37 ff is for charmm and Namd which is all atom ff using codes,,and
> gromacs is united atom so how can its results will be reliable as these are
> different things??.My protein of interest is having DNA..
> 

This does not make sense. What do you mean by “using codes”? And while gromacs 
can do united atom, all-atom force fields are routinely used with gromacs.

> Secondly how can i find ff parameters for my ligand of interest?? also if
> ff parameters are not in published form then it means i will not be able to
> use that ligand for MD run??
> 
> Regards..
> -- 
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[gmx-users] Hydrogen bond occupancy

[Neha Gupta]

Hi gromacs users,

What is meant by Hydrogen bond occupancy in protein ligand simulations?

What information do we extract from % of hydrogen bond occupancy?

Thanks,
Neha
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[gmx-users] determining restraints for pulling

[abhisek Mondal]

Hi,

I'm trying to pull a ligand from a protein-ligand complex. As per the
ligand-protein tutorial, I have restrained the ligand in topology file and
it looks like:

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include ligand topology
#include "drg.itp"

; Include position restraints
#ifdef POSRES_LIG
#include "posre_ACO.itp"
#endif

; Include water topology
#include "gromos43a1.ff/spc.itp"

In the md_pull.mdp, I'm using:

title   = Umbrella pulling simulation
define  = -DPOSRES
; Run parameters
integrator  = md;applying leap frog algorithm

So, is it proper for pulling ligand (ACO) from the protein or I'm doing
something wrong ? I'm really lost here, please help me out.

Thank you.


-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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Re: [gmx-users] Ligand simulation

[abhisek Mondal]

Check the total number of atoms at the top of topology files. If you have
made a complex manually then the numbers had to be accounted for.

On Wed, Apr 5, 2017 at 12:18 PM, RAHUL SURESH 
wrote:

> for Command
>
>
>
> *gmx grompp -f em.mdp -c solv.gro -p conformer.top -o ions.tpr*
> I get the following error.
>
>
> *Warning: atom name 5839 in conformer.top and solv.gro does not match (H81
> - 1H8)Warning: atom name 5840 in conformer.top and solv.gro does not match
> (H82 - 2H8)*
>
> Is it really an issue or can I use -maxwarn?
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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[gmx-users] Charmm ff compatibility with Gromacs

[maria khan]

Hello Gromacs users..

Charmm 37 ff is for charmm and Namd which is all atom ff using codes,,and
gromacs is united atom so how can its results will be reliable as these are
different things??.My protein of interest is having DNA..

Secondly how can i find ff parameters for my ligand of interest?? also if
ff parameters are not in published form then it means i will not be able to
use that ligand for MD run??

Regards..
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[gmx-users] Ligand simulation

[RAHUL SURESH]

for Command



*gmx grompp -f em.mdp -c solv.gro -p conformer.top -o ions.tpr*
I get the following error.


*Warning: atom name 5839 in conformer.top and solv.gro does not match (H81
- 1H8)Warning: atom name 5840 in conformer.top and solv.gro does not match
(H82 - 2H8)*

Is it really an issue or can I use -maxwarn?

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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[gmx-users] (no subject)

[RAHUL SURESH]

for Command



*gmx grompp -f em.mdp -c solv.gro -p conformer.top -o ions.tpr*
I get the following error.


*Warning: atom name 5839 in conformer.top and solv.gro does not match (H81
- 1H8)Warning: atom name 5840 in conformer.top and solv.gro does not match
(H82 - 2H8)*

Is it really an issue or can I use -maxwarn?


-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Regarding viewing Trajectories

[Mark Abraham]

Hi,

A peak in a distance distribution function by definition is contributed to
by lots of molecules around that distance from lots of different central
points. There's no single frame for each point.

If you look at a normal histogram, and see a peak, asking "which single
data point made this" is not meaningful, because multiple data points have
normally contributed.

Mark

On Wed, Apr 5, 2017 at 6:40 AM Dilip H N  wrote:

> Hello.,
> In RDF of amino acid with ammonia and water mixture, i have got a 1st peak,
> 2nd peak (solvation shell), and i need to view this in the vmd by making
> use of the trajectories (trr/xtc files), so while viewing the trajectories
>
> 1] how can i view that exact trajectory at which i have got the particular
> peak in RDF (since that would mean either H-bond formation/probability of
> tht molecule close to that)
> because viewing each frame to find it would take literally lot of time, ...
>
> Thank you.
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
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Re: [gmx-users] gmx insert-molecules - molecules "sticking out of the box"

[Mark Abraham]

Hi,

On Tue, Apr 4, 2017 at 10:02 AM Jernej Zidar  wrote:

> Hi,
>
> I am using 'gmx insert-molecules' to insert ten rather large polymer
> molecules into a 16x16x16 nm box. The problem is that the utility inserts
> the molecules randomly (which is good) in way that leaves the polymer
> molecules sticking outside the defined box and leaving lots of space empty.
>

As Magnus says, so long as the result honours the periodicity, which
representation is chosen is not of great importance (and readily changed
with trjconv).


> The manual lists a number of potential useful options under the switch
> "-selrpos" but the manual says nothing about what do the options do.
>

Ah, that could be improved. It likely relates to
http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html#gmx-insert-molecules,
and because it is common to several tools, is documented at
http://manual.gromacs.org/documentation/2016/onlinehelp/selections.html#specifying-selections-from-command-line
.


> How to instruct 'gmx insert-molecules' to keep the inserted molecules
> whole?
>

It did that already, right? :-)

Mark


> Thanks,
> Jernej
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Re: [gmx-users] continuation with different dt values

[Mark Abraham]

Hi,

You can do as you please, the data fields are all dumb. However some tools
will notice the discontinuity, or fail to notice, so I would encourage you
to avoid doing this unless there's some scientific reason that suggests it.

Mark

On Tue, 4 Apr 2017 00:04 Dayhoff, Guy  wrote:

> Hi,
>
>I’m continuing a run and setting init-step as the total steps completed
> in the run i’m continuing from,
> if I change the dt for the continuation do I need to scale the steps
> previously taken? i.e going from dt = 1
> to dt =2, completing 100 steps in the first sim, does init-step take the
> value 100 regardless of the change in dt?
>
> My Best,
>Guy Dayhoff
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Re: [gmx-users] XYZ file and obgmx

[Mark Abraham]

Hi,

Generally topology generators are specific to (groups of) force fields, so
switching force fields is almost the same as starting fresh.

Mark

On Tue, 4 Apr 2017 07:10 Lamm Gro  wrote:

> Dear Gromacs users ,
>
> I have a xyz file and I used OBGMX ( topology generator ) for that .
> Now I have itp and top file , but the problem is I want to change UFF
> forcefield ( that used by obgmx )  to gromacs forcefields like Amber03 .
> Can you please let me know how can i do that ?
>
> I am new in Gromacs and i hope you can help me .
>
> Regards,
> Saeed.
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Re: [gmx-users] No data on Pullf and Pullx files after restart

[Mark Abraham]

Hi,

That sounds like something an older version of GROMACS might have done.
Which is it? Does it happen with a new one?

Mark

On Tue, 4 Apr 2017 11:11 Souparno Adhikary  wrote:

> Hello,
>
> I restarted my umbrella sampling simulations using the tpbconv command. I
> used the -vel option in the command. It ran successfully. After that, when
> I am running the new simulations, pullf and pullx files are created for
> each sample but no data gets written in them.
>
> I am absolutely clueless how to solve this. Can you please help?
>
> Thanks in advance.
>
> Best regards,
>
> Souparno
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Re: [gmx-users] Force Fields Keeping sp3 Nitrogen Groups Planar?

[Mark Abraham]

Hi,

Amide nitrogen atoms are trigonal planar because the group is planar.
There's no free rotation about the n-c bond, and the lone pair forms a
hybrid orbital with the carbonyl.

Mark

On Tue, 4 Apr 2017 18:05 Phillip Rauscher  wrote:

> It occurs to me that an example would be helpful.  Here is an excerpt from
> the OPLS aminoacids.rtp file detailing alanine:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *[ ALA ] [ atoms ]  Nopls_238   -0.500 1 Hopls_241
> 0.300 1 CAopls_224B   0.140 1 HAopls_140
> 0.060 1 CBopls_135   -0.180 2HB1opls_140
> 0.060 2HB2opls_1400.060 2HB3opls_140
> 0.060 2  Copls_2350.500 3 Oopls_236
> -0.500 3 [ bonds ] N H NCACAHACACB
> CA CCB   HB1CB   HB2CB   HB3 C O-C N [
> impropers ]-CCA N Himproper_Z_N_X_Y CA+N
> C Oimproper_O_C_X_Y *
>
> We can see that the Nitrogen is bound to atoms H, CA, and -C (on the
> previous residue).  In the [impropers] section, an improper dihedral is
> defined for these four atoms (with the nitrogen in both of the dihedral
> planes).  If we look at the definition of that improper in the OPLS
> ffbonded.itp file, we see the following:
>
>
>
>
>
>
>
>
>
>
>
>
>
> *[ dihedraltypes ]; Improper OPLS dihedrals to keep groups planar.; (OPLS
> doesnt use impropers for chiral atoms).; Since these functions are periodic
> of the form 1-cos(2*x), they are actually; implemented as proper dihedrals
> [1+cos(2*x+180)] for the moment, ; to keep things compatible.; The defines
> are used in ffoplsaa.rtp or directly in your .top file; Z -N?-X -Y
> improper torsion#define improper_Z_N_X_Y180.0  4.18400   2*
> Given the functional form and the parameters used, this potential has
> minima at 0 and 180 degrees, thus keeping all four atoms (centered at the
> nitrogen) in the same plane.
>
> On Tue, Apr 4, 2017 at 10:38 AM, Phillip Rauscher  >
> wrote:
>
> > Hello all,
> >
> > I've noticed that in some of the force fields (in the aminoacid.rtp
> > files), an improper dihedral is applied to the nitrogens in the peptide
> > bond (and sometimes other amine groups as well), which are all sp3
> > hybridized with one lone pair.  Interestingly, the dihedral potential
> > parameters serve to keep the groups trigonal planar, rather than
> > tetrahedral.  More specifically, I've seen this in OPLS, Amber03, and
> > Charmm27 - enough to indicate that it's not a mistake (besides the fact
> > that it's applied to ALL amino acids!)  The functional form of the
> improper
> > potential varies between force fields, but the lowest energy angle is
> > always 0 or 180 indicating planar structure.
> >
> > Why is this done?  I've done some digging through the GROMACS
> publications
> > as well as those for the force fields and can't seem to find any
> reference
> > to this practice?  Is it an attempt to "average out" nitrogen inversions?
> > Is it just to eliminate a chiral center?
> >
> > Thanks for your help!
> >
> > -Phil Rauscher
> >
> > --
> > Phil Rauscher
> > Graduate Student
> > de Pablo and Rowan Research Groups
> > Institute for Molecular Engineering
> > University of Chicago
> >
>
>
>
> --
> Phil Rauscher
> Graduate Student
> de Pablo and Rowan Research Groups
> Institute for Molecular Engineering
> University of Chicago
> --
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