Re: [gmx-users] Fwd: Unusual bonding between residues in vmd

[ISHRAT JAHAN]

I have selected the whole system while writing the .xtc file and from that
.xtc file i wrote the gro file, then how there is mismatch b/w the
coordinates of  .xtc and .gro file.

On Tue, Aug 22, 2017 at 11:51 AM, Mark Abraham 
wrote:

> Hi,
>
> Probably there's a mismatch between the coordinate file you loaded in VMD
> and what's in the XTC. For example, you didn't write the ligand to the XTC.
>
> Mark
>
> On Tue, Aug 22, 2017 at 8:10 AM ISHRAT JAHAN  wrote:
>
> > -- Forwarded message --
> > From: ISHRAT JAHAN 
> > Date: Tue, Aug 22, 2017 at 11:35 AM
> > Subject: Unusual bonding between residues in vmd
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> >
> >
> > Dear all,
> > I was trying to do the simulation of 100 ns of protein and drug in
> gromacs
> > v- 5.1.4 using amber99sb.ff but i have stopped the simulation in between
> > i.e at 40 ns. By using 40 ns .xtc file i have generated .gro file after
> > applying pbc condition and when i load the .gro file in  Vmd i got the
> > followung error-
> > Warning) Unusual bond between residues:  509 (none) and 20136 (waters)
> > Warning) Unusual bond between residues:  509 (none) and 25255 (waters)
> > Warning) Unusual bond between residues:  509 (none) and 25255 (waters)
> > Warning) Unusual bond between residues:  509 (none) and 19182 (waters)
> > Warning) Unusual bond between residues:  509 (none) and 19206 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 12546 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 18490 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 18490 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 18557 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 19269 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 19281 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 19667 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 19667 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 25047 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 20005 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 20005 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 12450 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 12450 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 12928 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
> > Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
> >
> > Will anyone help me to solve the above problem.
> > Thanks in advance.
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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Re: [gmx-users] Fwd: Unusual bonding between residues in vmd

[ISHRAT JAHAN]

I have selected the whole system while writing the .xtc file and from that
.xtc file i wrote the gro file, then how there is mismatch b/w the
coordinates of  .xtc and .gro file.
My system appeared totally broken, unable to understand the error. please
help me to solve this problem.

On Tue, Aug 22, 2017 at 12:10 PM, ISHRAT JAHAN  wrote:

> I have selected the whole system while writing the .xtc file and from that
> .xtc file i wrote the gro file, then how there is mismatch b/w the
> coordinates of  .xtc and .gro file.
>
> On Tue, Aug 22, 2017 at 11:51 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> Probably there's a mismatch between the coordinate file you loaded in VMD
>> and what's in the XTC. For example, you didn't write the ligand to the
>> XTC.
>>
>> Mark
>>
>> On Tue, Aug 22, 2017 at 8:10 AM ISHRAT JAHAN  wrote:
>>
>> > -- Forwarded message --
>> > From: ISHRAT JAHAN 
>> > Date: Tue, Aug 22, 2017 at 11:35 AM
>> > Subject: Unusual bonding between residues in vmd
>> > To: gromacs.org_gmx-users@maillist.sys.kth.se
>> >
>> >
>> > Dear all,
>> > I was trying to do the simulation of 100 ns of protein and drug in
>> gromacs
>> > v- 5.1.4 using amber99sb.ff but i have stopped the simulation in between
>> > i.e at 40 ns. By using 40 ns .xtc file i have generated .gro file after
>> > applying pbc condition and when i load the .gro file in  Vmd i got the
>> > followung error-
>> > Warning) Unusual bond between residues:  509 (none) and 20136 (waters)
>> > Warning) Unusual bond between residues:  509 (none) and 25255 (waters)
>> > Warning) Unusual bond between residues:  509 (none) and 25255 (waters)
>> > Warning) Unusual bond between residues:  509 (none) and 19182 (waters)
>> > Warning) Unusual bond between residues:  509 (none) and 19206 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 12546 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 18490 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 18490 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 18557 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 19269 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 19281 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 19667 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 19667 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 25047 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 20005 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 20005 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 12450 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 12450 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 12928 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
>> > Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
>> >
>> > Will anyone help me to solve the above problem.
>> > Thanks in advance.
>> > --
>> > 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/Suppo

Re: [gmx-users] Regarding Unknown cmap torsion between atoms

[Dilip H N]

Hello,
1] it is the solute+Diglycine which is the constituting the mixture...
2] the method to create the system for both were the same...
the commands are...
gmx editconf -f Diglycinechimera2.gro -o Diglybox.gro -c -box x y z
(generating the box)
gmx insert-molecules -f Diglybox.gro -ci abc.gro -nmol 10 -o Dglyabc.gro
and for other system, gmx insert-molecules -f Diglybox.gro -ci def.gro
-nmol 10 -o Dglydef.gro (adding the solute molecules and getting the final
system)...
here the two solute .gro files are abc.gro and def.groand i have
followed the same procedure...
and thn gmx pdb2gmx -f Dglyabc.gro (or) gmx pdb2gmx -f Dglydef.gro...there
is [cmap] option in one topology file and in other topology there is no
[cmap] option...

How is it different thn..??






 Sent with Mailtrack


On Tue, Aug 22, 2017 at 11:49 AM, Mark Abraham 
wrote:

> Hi,
>
> Your description is too confused to follow. Your use of the words solvent
> and solute is unclear. pdb2gmx will never make a cmap that goes outside a
> moleculetype.
>
> If one use of pdb2gmx made a cmap and the other did not, then they were
> fundamentally different. If you don't know what was different, then you
> aren't doing science because you don't know what your method was. If so,
> start again and keep a record in a shell script this time.
>
> Mark
>
> On Tue, Aug 22, 2017 at 8:05 AM Dilip H N 
> wrote:
>
> > 1] in the line 8231 [ Unknown cmap torsion between atoms 8 10 12 15 18]
> it
> > is the diglycine peptide molecule only, it is stating the atomic numbers
> of
> > the diglycine molecule (8,10,12,15) and solute molecule (18)
> > 2] but one more problem is the Diglycine nitrogen and the solute
> containing
> > nitrogen are labelled as same (as N only)...
> > ie., atoms 8,10,12,15 (here atom 10 is N, and other atoms are  C, CA)
> > belong to diglycine and atom 18 belong to solute molecule of atom N, and
> > hence i am getting the error...i hope so(But with other system tht i
> > ran had no [cmap] in topology and the atoms in the solute were labelled
> > differentlyand ran correctly..)
> > 3] So can  i remove/delete the [cmap] line  (i tried removing cmap
> line
> > in topology..and thn with gmx grompp option it is workin fine..) does
> that
> > cause any error/manipulating the topology..etc..?? can i proceed removing
> > [cmap] is thr any harm..?
> > 4] I tried also with removing the last coloumn in [cmap] ie., removing
> 18,1
> > of am,funct..since as i told above the atom 18 is of the solute nitrogen
> > molecule which is labelled as same in the .rtp file in charmmFF, which is
> > causing the problemssince the gmx grompp is trying to bond wiht the
> > atom 18 N  which is solute and not Diglycine (since both N's are labelled
> > same)
> > [ cmap ]
> > ;  aiajakalam funct
> > 810121518 1
> > and edited and got it as:-
> >
> > [ cmap ]
> > ;  aiajakal
> > 8101215
> > and thn now if i run gmx grompp -f min.mdp -c mixture.gro -p topol.top -o
> > min.tpr
> >  it is showing:-
> >  WARNING 1 [file topol.top, line 8231]:
> >   Too few parameters on line (source file
> >
> > /home/dilip/Downloads/gromacs-2016.2/src/gromacs/
> gmxpreprocess/toppush.cpp,
> > line 2198)
> > So i tried with gmx grompp -f min.mdp -c mixture.gro -p topol.top -o
> > min.tpr -maxwarn 2 , and now it is working fine...
> >
> > So i have tried with different options..and i have discussed what i have
> > got..but are they the correct way...to proceed..??
> >
> > Any suggestions are welcome...
> >
> > Thank you...
> >
> >
> >  Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature&lang=en&;
> referral=cy16f01.di...@nitk.edu.in&idSignature=22
> > >
> >
> > On Mon, Aug 21, 2017 at 11:14 PM, Mark Abraham  >
> > wrote:
> >
> > > Hi,
> > >
> > > If your procedure for the two systems was actually the same, then the
> > error
> > > does not come from your solute. Unfortunately only you know what is on
> > line
> > > 8231... Work out what you did differently, e.g. by doing it again and
> > > making sure you do it the same way.
> > >
> > > Mark
> > >
> > > On Mon, Aug 21, 2017 at 7:27 PM Dilip H N 
> > > wrote:
> > >
> > > > 1] I created Diglycine peptide from chimera software, and got the
> .pdb
> > > > file, added two different solvents (A, B) and made two different
> > systems
> > > > say, A-(Diglycine+solvent1), B-(Diglycine+solvent2). I generated the
> > > > topology file from charmm36 FF by gmx pdb2gmx process for both the
> > > systems
> > > > A and B correctly (but in system A there is no [ cmap ] line in
> > topology,
> > > > but system B has [ cmap ] in topology).. Why is this in one system i
> am
> > > > getting but in other i am not..?  Is there any error...or what is
> it...
> > > >
> > > > 2] And  during gmx grompp  -f m

Re: [gmx-users] Fwd: Unusual bonding between residues in vmd

[Mark Abraham]

Hi,

Probably there's a mismatch between the coordinate file you loaded in VMD
and what's in the XTC. For example, you didn't write the ligand to the XTC.

Mark

On Tue, Aug 22, 2017 at 8:10 AM ISHRAT JAHAN  wrote:

> -- Forwarded message --
> From: ISHRAT JAHAN 
> Date: Tue, Aug 22, 2017 at 11:35 AM
> Subject: Unusual bonding between residues in vmd
> To: gromacs.org_gmx-users@maillist.sys.kth.se
>
>
> Dear all,
> I was trying to do the simulation of 100 ns of protein and drug in gromacs
> v- 5.1.4 using amber99sb.ff but i have stopped the simulation in between
> i.e at 40 ns. By using 40 ns .xtc file i have generated .gro file after
> applying pbc condition and when i load the .gro file in  Vmd i got the
> followung error-
> Warning) Unusual bond between residues:  509 (none) and 20136 (waters)
> Warning) Unusual bond between residues:  509 (none) and 25255 (waters)
> Warning) Unusual bond between residues:  509 (none) and 25255 (waters)
> Warning) Unusual bond between residues:  509 (none) and 19182 (waters)
> Warning) Unusual bond between residues:  509 (none) and 19206 (waters)
> Warning) Unusual bond between residues:  510 (none) and 12546 (waters)
> Warning) Unusual bond between residues:  510 (none) and 18490 (waters)
> Warning) Unusual bond between residues:  510 (none) and 18490 (waters)
> Warning) Unusual bond between residues:  510 (none) and 18557 (waters)
> Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
> Warning) Unusual bond between residues:  510 (none) and 19269 (waters)
> Warning) Unusual bond between residues:  510 (none) and 19281 (waters)
> Warning) Unusual bond between residues:  510 (none) and 19667 (waters)
> Warning) Unusual bond between residues:  510 (none) and 19667 (waters)
> Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
> Warning) Unusual bond between residues:  510 (none) and 25047 (waters)
> Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
> Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
> Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
> Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
> Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
> Warning) Unusual bond between residues:  510 (none) and 20005 (waters)
> Warning) Unusual bond between residues:  510 (none) and 20005 (waters)
> Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
> Warning) Unusual bond between residues:  510 (none) and 12450 (waters)
> Warning) Unusual bond between residues:  510 (none) and 12450 (waters)
> Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
> Warning) Unusual bond between residues:  510 (none) and 12928 (waters)
> Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
> Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
> Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
> Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
> Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
> Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
> Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
> Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
> Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
> Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
>
> Will anyone help me to solve the above problem.
> Thanks in advance.
> --
> 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] Regarding Unknown cmap torsion between atoms

[Mark Abraham]

Hi,

Your description is too confused to follow. Your use of the words solvent
and solute is unclear. pdb2gmx will never make a cmap that goes outside a
moleculetype.

If one use of pdb2gmx made a cmap and the other did not, then they were
fundamentally different. If you don't know what was different, then you
aren't doing science because you don't know what your method was. If so,
start again and keep a record in a shell script this time.

Mark

On Tue, Aug 22, 2017 at 8:05 AM Dilip H N  wrote:

> 1] in the line 8231 [ Unknown cmap torsion between atoms 8 10 12 15 18] it
> is the diglycine peptide molecule only, it is stating the atomic numbers of
> the diglycine molecule (8,10,12,15) and solute molecule (18)
> 2] but one more problem is the Diglycine nitrogen and the solute containing
> nitrogen are labelled as same (as N only)...
> ie., atoms 8,10,12,15 (here atom 10 is N, and other atoms are  C, CA)
> belong to diglycine and atom 18 belong to solute molecule of atom N, and
> hence i am getting the error...i hope so(But with other system tht i
> ran had no [cmap] in topology and the atoms in the solute were labelled
> differentlyand ran correctly..)
> 3] So can  i remove/delete the [cmap] line  (i tried removing cmap line
> in topology..and thn with gmx grompp option it is workin fine..) does that
> cause any error/manipulating the topology..etc..?? can i proceed removing
> [cmap] is thr any harm..?
> 4] I tried also with removing the last coloumn in [cmap] ie., removing 18,1
> of am,funct..since as i told above the atom 18 is of the solute nitrogen
> molecule which is labelled as same in the .rtp file in charmmFF, which is
> causing the problemssince the gmx grompp is trying to bond wiht the
> atom 18 N  which is solute and not Diglycine (since both N's are labelled
> same)
> [ cmap ]
> ;  aiajakalam funct
> 810121518 1
> and edited and got it as:-
>
> [ cmap ]
> ;  aiajakal
> 8101215
> and thn now if i run gmx grompp -f min.mdp -c mixture.gro -p topol.top -o
> min.tpr
>  it is showing:-
>  WARNING 1 [file topol.top, line 8231]:
>   Too few parameters on line (source file
>
> /home/dilip/Downloads/gromacs-2016.2/src/gromacs/gmxpreprocess/toppush.cpp,
> line 2198)
> So i tried with gmx grompp -f min.mdp -c mixture.gro -p topol.top -o
> min.tpr -maxwarn 2 , and now it is working fine...
>
> So i have tried with different options..and i have discussed what i have
> got..but are they the correct way...to proceed..??
>
> Any suggestions are welcome...
>
> Thank you...
>
>
>  Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22
> >
>
> On Mon, Aug 21, 2017 at 11:14 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > If your procedure for the two systems was actually the same, then the
> error
> > does not come from your solute. Unfortunately only you know what is on
> line
> > 8231... Work out what you did differently, e.g. by doing it again and
> > making sure you do it the same way.
> >
> > Mark
> >
> > On Mon, Aug 21, 2017 at 7:27 PM Dilip H N 
> > wrote:
> >
> > > 1] I created Diglycine peptide from chimera software, and got the .pdb
> > > file, added two different solvents (A, B) and made two different
> systems
> > > say, A-(Diglycine+solvent1), B-(Diglycine+solvent2). I generated the
> > > topology file from charmm36 FF by gmx pdb2gmx process for both the
> > systems
> > > A and B correctly (but in system A there is no [ cmap ] line in
> topology,
> > > but system B has [ cmap ] in topology).. Why is this in one system i am
> > > getting but in other i am not..?  Is there any error...or what is it...
> > >
> > > 2] And  during gmx grompp  -f min.mdp -c mixture.gro -p topol.top -o
> > > min.tpr
> > >
> > > for system A (whr there is no [cmap] in topology), the gmx grompp
> command
> > > works well...
> > > But for system B (which has [cmap] in topology), the error comes as:-
> > >
> > > > ERROR 1 [file topol.top, line 8231]:
> > > >  Unknown cmap torsion between atoms 8 10 12 15 18
> > >
> > > How can i solve this ...??
> > >
> > > Thank you...
> > >
> > >
> > > On Mon, Aug 21, 2017 at 10:18 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> > >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > On Mon, Aug 21, 2017 at 6:33 PM Dilip H N  >
> > > > wrote:
> > > >
> > > > > Hello,
> > > > > I have created a peptide from chimera software and got the pdb
> file,
> > > and
> > > > i
> > > > > have added solvents to it the resultant is mixture.gro, and used
> gmx
> > > > > pdb2gmx to generate the topology using charmm36 FF. I got the
> > topology
> > > > > correct, but nw if i give the command for energy minimization :-
> > > > > gmx grompp -f min.mdp -c mixture.gro -p topol.top -o min.tpr
> > > > >
> > > > > I am getting error as:-
> > > > >
> > > > > NOTE 1 [file min.mdp]:
> > > > >   With Verlet lists the optimal nstlist is >= 10,

[gmx-users] Fwd: Unusual bonding between residues in vmd

[ISHRAT JAHAN]

-- Forwarded message --
From: ISHRAT JAHAN 
Date: Tue, Aug 22, 2017 at 11:35 AM
Subject: Unusual bonding between residues in vmd
To: gromacs.org_gmx-users@maillist.sys.kth.se


Dear all,
I was trying to do the simulation of 100 ns of protein and drug in gromacs
v- 5.1.4 using amber99sb.ff but i have stopped the simulation in between
i.e at 40 ns. By using 40 ns .xtc file i have generated .gro file after
applying pbc condition and when i load the .gro file in  Vmd i got the
followung error-
Warning) Unusual bond between residues:  509 (none) and 20136 (waters)
Warning) Unusual bond between residues:  509 (none) and 25255 (waters)
Warning) Unusual bond between residues:  509 (none) and 25255 (waters)
Warning) Unusual bond between residues:  509 (none) and 19182 (waters)
Warning) Unusual bond between residues:  509 (none) and 19206 (waters)
Warning) Unusual bond between residues:  510 (none) and 12546 (waters)
Warning) Unusual bond between residues:  510 (none) and 18490 (waters)
Warning) Unusual bond between residues:  510 (none) and 18490 (waters)
Warning) Unusual bond between residues:  510 (none) and 18557 (waters)
Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
Warning) Unusual bond between residues:  510 (none) and 19269 (waters)
Warning) Unusual bond between residues:  510 (none) and 19281 (waters)
Warning) Unusual bond between residues:  510 (none) and 19667 (waters)
Warning) Unusual bond between residues:  510 (none) and 19667 (waters)
Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
Warning) Unusual bond between residues:  510 (none) and 25047 (waters)
Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
Warning) Unusual bond between residues:  510 (none) and 20005 (waters)
Warning) Unusual bond between residues:  510 (none) and 20005 (waters)
Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
Warning) Unusual bond between residues:  510 (none) and 12450 (waters)
Warning) Unusual bond between residues:  510 (none) and 12450 (waters)
Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
Warning) Unusual bond between residues:  510 (none) and 12928 (waters)
Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
Warning) Unusual bond between residues:  510 (none) and 24324 (waters)
Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
Warning) Unusual bond between residues:  510 (none) and 12454 (waters)
Warning) Unusual bond between residues:  510 (none) and 18599 (waters)
Warning) Unusual bond between residues:  510 (none) and 19248 (waters)
Warning) Unusual bond between residues:  510 (none) and 24324 (waters)

Will anyone help me to solve the above problem.
Thanks in advance.
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Re: [gmx-users] Regarding Unknown cmap torsion between atoms

[Dilip H N]

1] in the line 8231 [ Unknown cmap torsion between atoms 8 10 12 15 18] it
is the diglycine peptide molecule only, it is stating the atomic numbers of
the diglycine molecule (8,10,12,15) and solute molecule (18)
2] but one more problem is the Diglycine nitrogen and the solute containing
nitrogen are labelled as same (as N only)...
ie., atoms 8,10,12,15 (here atom 10 is N, and other atoms are  C, CA)
belong to diglycine and atom 18 belong to solute molecule of atom N, and
hence i am getting the error...i hope so(But with other system tht i
ran had no [cmap] in topology and the atoms in the solute were labelled
differentlyand ran correctly..)
3] So can  i remove/delete the [cmap] line  (i tried removing cmap line
in topology..and thn with gmx grompp option it is workin fine..) does that
cause any error/manipulating the topology..etc..?? can i proceed removing
[cmap] is thr any harm..?
4] I tried also with removing the last coloumn in [cmap] ie., removing 18,1
of am,funct..since as i told above the atom 18 is of the solute nitrogen
molecule which is labelled as same in the .rtp file in charmmFF, which is
causing the problemssince the gmx grompp is trying to bond wiht the
atom 18 N  which is solute and not Diglycine (since both N's are labelled
same)
[ cmap ]
;  aiajakalam funct
810121518 1
and edited and got it as:-

[ cmap ]
;  aiajakal
8101215
and thn now if i run gmx grompp -f min.mdp -c mixture.gro -p topol.top -o
min.tpr
 it is showing:-
 WARNING 1 [file topol.top, line 8231]:
  Too few parameters on line (source file

/home/dilip/Downloads/gromacs-2016.2/src/gromacs/gmxpreprocess/toppush.cpp,
line 2198)
So i tried with gmx grompp -f min.mdp -c mixture.gro -p topol.top -o
min.tpr -maxwarn 2 , and now it is working fine...

So i have tried with different options..and i have discussed what i have
got..but are they the correct way...to proceed..??

Any suggestions are welcome...

Thank you...


 Sent with Mailtrack


On Mon, Aug 21, 2017 at 11:14 PM, Mark Abraham 
wrote:

> Hi,
>
> If your procedure for the two systems was actually the same, then the error
> does not come from your solute. Unfortunately only you know what is on line
> 8231... Work out what you did differently, e.g. by doing it again and
> making sure you do it the same way.
>
> Mark
>
> On Mon, Aug 21, 2017 at 7:27 PM Dilip H N 
> wrote:
>
> > 1] I created Diglycine peptide from chimera software, and got the .pdb
> > file, added two different solvents (A, B) and made two different systems
> > say, A-(Diglycine+solvent1), B-(Diglycine+solvent2). I generated the
> > topology file from charmm36 FF by gmx pdb2gmx process for both the
> systems
> > A and B correctly (but in system A there is no [ cmap ] line in topology,
> > but system B has [ cmap ] in topology).. Why is this in one system i am
> > getting but in other i am not..?  Is there any error...or what is it...
> >
> > 2] And  during gmx grompp  -f min.mdp -c mixture.gro -p topol.top -o
> > min.tpr
> >
> > for system A (whr there is no [cmap] in topology), the gmx grompp command
> > works well...
> > But for system B (which has [cmap] in topology), the error comes as:-
> >
> > > ERROR 1 [file topol.top, line 8231]:
> > >  Unknown cmap torsion between atoms 8 10 12 15 18
> >
> > How can i solve this ...??
> >
> > Thank you...
> >
> >
> > On Mon, Aug 21, 2017 at 10:18 PM, Mark Abraham  >
> > wrote:
> >
> > > Hi,
> > >
> > > On Mon, Aug 21, 2017 at 6:33 PM Dilip H N 
> > > wrote:
> > >
> > > > Hello,
> > > > I have created a peptide from chimera software and got the pdb file,
> > and
> > > i
> > > > have added solvents to it the resultant is mixture.gro, and used gmx
> > > > pdb2gmx to generate the topology using charmm36 FF. I got the
> topology
> > > > correct, but nw if i give the command for energy minimization :-
> > > > gmx grompp -f min.mdp -c mixture.gro -p topol.top -o min.tpr
> > > >
> > > > I am getting error as:-
> > > >
> > > > NOTE 1 [file min.mdp]:
> > > >   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20.
> Note
> > > >   that with the Verlet scheme, nstlist has no effect on the accuracy
> of
> > > >   your simulation.
> > > >
> > > > Setting the LD random seed to -1490567170
> > > > Generated 97877 of the 97903 non-bonded parameter combinations
> > > > Generating 1-4 interactions: fudge = 1
> > > > Generated 64492 of the 97903 1-4 parameter combinations
> > > >
> > > > ERROR 1 [file topol.top, line 8231]:
> > > >   Unknown cmap torsion between atoms 8 10 12 15 18
> > > >
> > > > There was 1 note
> > > > ---
> > > > Program: gmx grompp, version 2016.3
> > > > Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1622)
> > > >
> > > > Fatal error:
> > > > There was 1 error in input fil

Re: [gmx-users] FEP calculations on multiple nodes

[Nikhil Maroli]

Okay, you might need to consider

gmx mdrun -v -ntmpi XX -ntomp XX -deffnm   -gpu_id XXX



http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html

http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm
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Re: [gmx-users] Average and bfactors.pdb

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; } Hi justin
Thank you so much for replyingAccording to the gromacs tuturial, i am trying to 
analyse my complex in terms of RMSD. In order to do that, first it is needed to 
obtain the average structure to get RMSD vs average structure . And average 
structure is a side product of obtaining RMSF. Is there anyway that i can 
calculate RMSD instead of geting RMSD vs average structure? If you want to 
caculate RMSD , wont you perform this way? 
Thanks in advanceFarial

Sent from Yahoo Mail for iPhone


On Monday, August 21, 2017, 5:24 PM, Justin Lemkul  wrote:



On 8/20/17 11:48 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Dear justin
> Thank you for your replyIt means, there is no problem, i can ignore it ang go 
> ahead?

Sure, but keep in mind that this "average structure" has no physical 
meaning.  The B-factors are (possibly) useful, but also keep in mind 
that solution dynamics and crystal dynamics are very different, so 
comparing the two may or may not be useful.

-Justin
> Sent from Yahoo Mail for iPhone
>
>
> On Monday, August 21, 2017, 2:34 AM, Justin Lemkul  wrote:
>
>
>
> On 8/20/17 11:51 AM, farial tavakoli wrote:
>>    blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>>!important; }  Dear gmx users
>> I removed jumps from my .xtc file before by using gmx trjconv and viewed my 
>> complex in vmd, it was ok and rhere was no jump. Now i use gmx rmsf and the 
>> same .xtc file which was created after using gmx trjconv, but when i view 
>> average. Pdb and bfactors.pdb files in pymol, my protein is still brocken. 
>> Would you please advice me how to solve this problem?
> There is no physical significance to an average set of coordinates.  These may
> appear broken or distorted.
>
> http://www.gromacs.org/Documentation/Terminology/Average_Structure
>
> -Justin
>

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] FEP calculations on multiple nodes

[Vikas Dubey]

Hi,

That's exactly the problem. There is no error except segmentation fault. I
have provided the *.log file link below if that helps.



https://filetea.me/n3wNaRevmeUS8iFWrIs4UlHfQ

On 21 August 2017 at 19:12, Nikhil Maroli  wrote:

> Hi,
>
> Where and What is the error?  It is better to upload the file somewhere and
> providing a link here.
> --
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[gmx-users] Trouble with gmx distance

[Sotirios Dionysios I. Papadatos]

Hi, I am trying to calculate the distance between two atoms, which are defined 
in an index file. The command that I use is:

"gmx distance -f output.gro -s prod.tpr -n index.ndx -oav distance.xvg"

I get the obvious:

"Selection 'atom_name' does not evaluate into an even number of positions (there

are 1 positions)"
The same happens if I use in -f prod.trr
What might be wrong? Any insights on what to look for? What usually gives this 
kind of error?
Feel free to ask for any further information.
Thanks in advance
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Re: [gmx-users] Regarding Unknown cmap torsion between atoms

[Mark Abraham]

Hi,

If your procedure for the two systems was actually the same, then the error
does not come from your solute. Unfortunately only you know what is on line
8231... Work out what you did differently, e.g. by doing it again and
making sure you do it the same way.

Mark

On Mon, Aug 21, 2017 at 7:27 PM Dilip H N  wrote:

> 1] I created Diglycine peptide from chimera software, and got the .pdb
> file, added two different solvents (A, B) and made two different systems
> say, A-(Diglycine+solvent1), B-(Diglycine+solvent2). I generated the
> topology file from charmm36 FF by gmx pdb2gmx process for both the systems
> A and B correctly (but in system A there is no [ cmap ] line in topology,
> but system B has [ cmap ] in topology).. Why is this in one system i am
> getting but in other i am not..?  Is there any error...or what is it...
>
> 2] And  during gmx grompp  -f min.mdp -c mixture.gro -p topol.top -o
> min.tpr
>
> for system A (whr there is no [cmap] in topology), the gmx grompp command
> works well...
> But for system B (which has [cmap] in topology), the error comes as:-
>
> > ERROR 1 [file topol.top, line 8231]:
> >  Unknown cmap torsion between atoms 8 10 12 15 18
>
> How can i solve this ...??
>
> Thank you...
>
>
> On Mon, Aug 21, 2017 at 10:18 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > On Mon, Aug 21, 2017 at 6:33 PM Dilip H N 
> > wrote:
> >
> > > Hello,
> > > I have created a peptide from chimera software and got the pdb file,
> and
> > i
> > > have added solvents to it the resultant is mixture.gro, and used gmx
> > > pdb2gmx to generate the topology using charmm36 FF. I got the topology
> > > correct, but nw if i give the command for energy minimization :-
> > > gmx grompp -f min.mdp -c mixture.gro -p topol.top -o min.tpr
> > >
> > > I am getting error as:-
> > >
> > > NOTE 1 [file min.mdp]:
> > >   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
> > >   that with the Verlet scheme, nstlist has no effect on the accuracy of
> > >   your simulation.
> > >
> > > Setting the LD random seed to -1490567170
> > > Generated 97877 of the 97903 non-bonded parameter combinations
> > > Generating 1-4 interactions: fudge = 1
> > > Generated 64492 of the 97903 1-4 parameter combinations
> > >
> > > ERROR 1 [file topol.top, line 8231]:
> > >   Unknown cmap torsion between atoms 8 10 12 15 18
> > >
> > > There was 1 note
> > > ---
> > > Program: gmx grompp, version 2016.3
> > > Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1622)
> > >
> > > Fatal error:
> > > There was 1 error in input file(s)
> > >
> > > 1] What is this cmap all about..??
> > >
> >
> > That's part of how the CHARMM force field works for modelling peptides.
> You
> > should have a basic understanding of that from your background reading
> that
> > led to the choice of this force field.
> >
> >
> > > 2] How do i correct this error..?
> > >
> >
> > Whether you can do so depends whether chimera has generated a structure
> > that has a valid CHARMM36 representation, ie there exists a CMAP
> definition
> > for the types of those atoms.
> >
> > Mark
> >
> >
> > > Any suggestions will be helpful...
> > >
> > > Thank you...
> > >
> > >
> > >
> > >
> > > --
> > > With Best Regards,
> > >
> > > DILIP.H.N
> > > Ph.D Student
> > > --
> > > 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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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
> --
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Re: [gmx-users] Regarding Unknown cmap torsion between atoms

[Dilip H N]

1] I created Diglycine peptide from chimera software, and got the .pdb
file, added two different solvents (A, B) and made two different systems
say, A-(Diglycine+solvent1), B-(Diglycine+solvent2). I generated the
topology file from charmm36 FF by gmx pdb2gmx process for both the systems
A and B correctly (but in system A there is no [ cmap ] line in topology,
but system B has [ cmap ] in topology).. Why is this in one system i am
getting but in other i am not..?  Is there any error...or what is it...

2] And  during gmx grompp  -f min.mdp -c mixture.gro -p topol.top -o min.tpr

for system A (whr there is no [cmap] in topology), the gmx grompp command
works well...
But for system B (which has [cmap] in topology), the error comes as:-

> ERROR 1 [file topol.top, line 8231]:
>  Unknown cmap torsion between atoms 8 10 12 15 18

How can i solve this ...??

Thank you...


On Mon, Aug 21, 2017 at 10:18 PM, Mark Abraham 
wrote:

> Hi,
>
> On Mon, Aug 21, 2017 at 6:33 PM Dilip H N 
> wrote:
>
> > Hello,
> > I have created a peptide from chimera software and got the pdb file, and
> i
> > have added solvents to it the resultant is mixture.gro, and used gmx
> > pdb2gmx to generate the topology using charmm36 FF. I got the topology
> > correct, but nw if i give the command for energy minimization :-
> > gmx grompp -f min.mdp -c mixture.gro -p topol.top -o min.tpr
> >
> > I am getting error as:-
> >
> > NOTE 1 [file min.mdp]:
> >   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
> >   that with the Verlet scheme, nstlist has no effect on the accuracy of
> >   your simulation.
> >
> > Setting the LD random seed to -1490567170
> > Generated 97877 of the 97903 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 1
> > Generated 64492 of the 97903 1-4 parameter combinations
> >
> > ERROR 1 [file topol.top, line 8231]:
> >   Unknown cmap torsion between atoms 8 10 12 15 18
> >
> > There was 1 note
> > ---
> > Program: gmx grompp, version 2016.3
> > Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1622)
> >
> > Fatal error:
> > There was 1 error in input file(s)
> >
> > 1] What is this cmap all about..??
> >
>
> That's part of how the CHARMM force field works for modelling peptides. You
> should have a basic understanding of that from your background reading that
> led to the choice of this force field.
>
>
> > 2] How do i correct this error..?
> >
>
> Whether you can do so depends whether chimera has generated a structure
> that has a valid CHARMM36 representation, ie there exists a CMAP definition
> for the types of those atoms.
>
> Mark
>
>
> > Any suggestions will be helpful...
> >
> > Thank you...
> >
> >
> >
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> > --
> > 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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Ph.D Student
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Re: [gmx-users] FEP calculations on multiple nodes

[Nikhil Maroli]

Hi,

Where and What is the error?  It is better to upload the file somewhere and
providing a link here.
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Re: [gmx-users] Regarding Unknown cmap torsion between atoms

[Mark Abraham]

Hi,

On Mon, Aug 21, 2017 at 6:33 PM Dilip H N  wrote:

> Hello,
> I have created a peptide from chimera software and got the pdb file, and i
> have added solvents to it the resultant is mixture.gro, and used gmx
> pdb2gmx to generate the topology using charmm36 FF. I got the topology
> correct, but nw if i give the command for energy minimization :-
> gmx grompp -f min.mdp -c mixture.gro -p topol.top -o min.tpr
>
> I am getting error as:-
>
> NOTE 1 [file min.mdp]:
>   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>   that with the Verlet scheme, nstlist has no effect on the accuracy of
>   your simulation.
>
> Setting the LD random seed to -1490567170
> Generated 97877 of the 97903 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 64492 of the 97903 1-4 parameter combinations
>
> ERROR 1 [file topol.top, line 8231]:
>   Unknown cmap torsion between atoms 8 10 12 15 18
>
> There was 1 note
> ---
> Program: gmx grompp, version 2016.3
> Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1622)
>
> Fatal error:
> There was 1 error in input file(s)
>
> 1] What is this cmap all about..??
>

That's part of how the CHARMM force field works for modelling peptides. You
should have a basic understanding of that from your background reading that
led to the choice of this force field.


> 2] How do i correct this error..?
>

Whether you can do so depends whether chimera has generated a structure
that has a valid CHARMM36 representation, ie there exists a CMAP definition
for the types of those atoms.

Mark


> Any suggestions will be helpful...
>
> Thank you...
>
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
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[gmx-users] Regarding Unknown cmap torsion between atoms

[Dilip H N]

Hello,
I have created a peptide from chimera software and got the pdb file, and i
have added solvents to it the resultant is mixture.gro, and used gmx
pdb2gmx to generate the topology using charmm36 FF. I got the topology
correct, but nw if i give the command for energy minimization :-
gmx grompp -f min.mdp -c mixture.gro -p topol.top -o min.tpr

I am getting error as:-

NOTE 1 [file min.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to -1490567170
Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations

ERROR 1 [file topol.top, line 8231]:
  Unknown cmap torsion between atoms 8 10 12 15 18

There was 1 note
---
Program: gmx grompp, version 2016.3
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1622)

Fatal error:
There was 1 error in input file(s)

1] What is this cmap all about..??
2] How do i correct this error..?

Any suggestions will be helpful...

Thank you...




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With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] FEP calculations on multiple nodes

[Vikas Dubey]

Hi Micheal,





** What does the logfile say that was output?*
*Ans : Log file output while running on PC (with command gmx mdrun -deffnm
md_0 -nt 36 ).  :*

Using GPU 8x8 non-bonded kernels

Removing pbc first time
Pinning threads with an auto-selected logical core stride of 1

Initializing Parallel LINear Constraint Solver

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 116-122
  --- Thank You ---  

The number of constraints is 36872
There are inter charge-group constraints,
will communicate selected coordinates each lincs iteration
9303 constraints are involved in constraint triangles,
will apply an additional matrix expansion of order 6 for couplings
between constraints inside triangles

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
  --- Thank You ---  


Linking all bonded interactions to atoms
There are 45357 inter charge-group virtual sites,
will an extra communication step for selected coordinates and forces

The initial number of communication pulses is: X 1 Y 1 Z 1
The initial domain decomposition cell size is: X 6.03 nm Y 3.02 nm Z 9.20 nm

The maximum allowed distance for charge groups involved in interactions is:
 non-bonded interactions   1.261 nm
(the following are initial values, they could change due to box deformation)
two-body bonded interactions  (-rdd)   1.261 nm
  multi-body bonded interactions  (-rdd)   1.261 nm
  virtual site constructions  (-rcon)  3.016 nm
  atoms separated by up to 7 constraints  (-rcon)  3.016 nm

When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1 Z 1
The minimum size for domain decomposition cells is 1.261 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.21 Y 0.42 Z 0.14
The maximum allowed distance for charge groups involved in interactions is:
 non-bonded interactions   1.261 nm
two-body bonded interactions  (-rdd)   1.261 nm
  multi-body bonded interactions  (-rdd)   1.261 nm
  virtual site constructions  (-rcon)  1.261 nm
  atoms separated by up to 7 constraints  (-rcon)  1.261 nm


Making 3D domain decomposition grid 2 x 4 x 2, home cell index 0 0 0

Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  System

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
  --- Thank You ---  
-



** What command are you using to run on multiple nodes ? *

*I use following script on the cluster. Last line indicates the command. *


#SBATCH --job-name=2_1_0
#SBATCH --mail-type=ALL
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --ntasks-per-core=2
#SBATCH --cpus-per-task=4
#SBATCH --constraint=gpu
#SBATCH --output out.txt
#SBATCH --error  err.txt
#
# load modules and run simulation
module load daint-gpu
module load GROMACS
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
export CRAY_CUDA_MPS=1

srun -n $SLURM_NTASKS --ntasks-per-node=$SLURM_NTASKS_PER_NODE -c
$SLURM_CPUS_PER_TASK gmx_mpi mdrun -deffnm md_0


-


** What is the .mdp file?*


My general *.mdp file is similar to what has been described here, apart
from certain changes for protein-membrane system:


http://wwwuser.gwdg.de/~ggroenh/exercise_html/exercise1.html

---


** How many nodes are you running on?*

Simulation runs fine on one node with 24 cores.  I want to run each windows
on maybe 2-3 nodes.  I have tried running simulation on my desktop using
"-nt" flag. It works fine until -nt 30. After that simulation crashes.

---

Re: [gmx-users] FEP calculations on multiple nodes

[Michael Shirts]

Significantly more information is be needed to understand what happened.

* What does the logfile say that was output?
* What command are you using to run on multiple nodes?
* What is the .mdp file?
* How many nodes are you running on?
* What version of the program?

And so forth.

On Mon, Aug 21, 2017 at 4:49 AM, Vikas Dubey 
wrote:

> Hi everyone,
>
> I am trying runa  FEP calculation with a system of ~25 particles. I
> have 20 windows and I am currently running my simulations on 1 node each.
> Since, my system is big, I just get 2.5ns in day. So, I thought to run each
> of my window on multiple nodes but for some reason, it crashes immediately
> after starting with an error.
>
>
> *Segmentation fault (core dumped)*
>
> Simulations run smoothly on one node. No error there. I tried to see file
> but there was nothing written there. Any help would be very much
> appreciated.
>
>
> Thanks,
> Vikas
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Re: [gmx-users] Residue 1 mapping problem?

[Justin Lemkul]

On 8/21/17 6:20 AM, morpheus wrote:

Hi,

I would like to simulate chain D and E of pdb-id 1oga but pdb2gmx complains
about the first (?) residues of the 2 chains:

"WARNING: WARNING: Residue 1 named GLN of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed."


This is an overly verbose message, which should not actually be a 
"warning."  Because you're requesting normal terminal patching (e.g. 
NH3+), the H of residue 1 is deleted and will be replaced with H[123].  
So this is really just telling you that's going on.  It really shouldn't 
be displayed, because it's confusing.  But you receive no errors and you 
can see that the topology was successfully generated.


-Justin


I assume it means this GLN (as it is the first residue of the file):

ATOM   3164  N   GLN D   3  22.890 -35.428 -11.393  1.00
22.91   N
ATOM   3165  CA  GLN D   3  21.681 -35.958 -10.698  1.00
21.34   C
ATOM   3166  C   GLN D   3  20.599 -36.345 -11.695  1.00
20.99   C
ATOM   3167  O   GLN D   3  20.336 -35.616 -12.646  1.00
22.83   O
ATOM   3168  CB  GLN D   3  21.091 -34.889  -9.797  1.00
20.05   C
ATOM   3169  CG  GLN D   3  21.926 -34.493  -8.608  1.00
20.82   C
ATOM   3170  CD  GLN D   3  21.388 -33.220  -8.008  1.00
19.14   C
ATOM   3171  OE1 GLN D   3  21.602 -32.139  -8.553  1.00
21.07   O
ATOM   3172  NE2 GLN D   3  20.653 -33.341  -6.916  1.00
21.18   N
ATOM   3173  N   LEU D   4  19.949 -37.480 -11.445  1.00
21.46   N
ATOM   3174  CA  LEU D   4  18.889 -37.992 -12.300  1.00
22.61   C
ATOM   3175  C   LEU D   4  17.679 -38.428 -11.487  1.00
20.04   C
ATOM   3176  O   LEU D   4  17.814 -38.838 -10.337  1.00
21.78   O
ATOM   3177  CB  LEU D   4  19.386 -39.229 -13.059  1.00
22.96   C
ATOM   3178  CG  LEU D   4  20.637 -39.103 -13.912  1.00
26.17   C
ATOM   3179  CD1 LEU D   4  21.062 -40.497 -14.412  1.00
29.25   C
ATOM   3180  CD2 LEU D   4  20.341 -38.189 -15.071  1.00
27.56   C

Any ideas? My commands and gromacs output below.

Thanks!



[b@localhost newTry]$ gmx pdb2gmx -f JM22_fullMHC_fullTCR.pdb -o
JM22_fullMHC_fullTCR.gro -p JM22_fullMHC_fullTCR.top -i
JM22_fullMHC_fullTCR.posre.itp -ignh -vsite hydrogens
  :-) GROMACS - gmx pdb2gmx, 2016.2 (-:

 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) 2001-2015, 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 2016.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Working dir:
/home/b/data/projects/anton_mutationsMHC/complexes_withConstTcrRegions/JM22_onlyTCR/newTry
Command line:
   gmx pdb2gmx -f JM22_fullMHC_fullTCR.pdb -o JM22_fullMHC_fullTCR.gro -p
JM22_fullMHC_fullTCR.top -i JM22_fullMHC_fullTCR.posre.itp -ignh -vsite
hydrogens


Select the Force Field:
 From '/usr/share/gromacs/top':
  1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
1999-2012, 2003)
  2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
  3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29,
461-469, 1996)
  4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
1049-1074, 2000)
  5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
712-725, 2006)
  6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
Proteins 78, 1950-58, 2010)
  7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
  8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
  9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force fi

Re: [gmx-users] Error in simulated annealing

[Justin Lemkul]

On 8/21/17 2:42 AM, Seera Suryanarayana wrote:

Dear gromacs users,
I wanted to do simulated annealing and I set up the .mdp file as follow...

title   = OPLS 4qam MD simulation
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5000  ; 2 * 5000 = 50 ps (100 ns)
dt  = 0.002 ; 2 fs
; Output control
nstxout = 5 ; save coordinates every 100.0 ps
nstvout = 5 ; save velocities every 100.0 ps
nstenergy   = 5 ; save energies every 100.0 ps
nstlog  = 5 ; update log file every 100.0 ps
nstxout-compressed  = 5  ; save compressed coordinates every 100.0
ps
 ; nstxout-compressed replaces nstxtcout
compressed-x-grps   = System; replaces xtc-grps
; Bond parameters
continuation= yes   ; Restarting after NPT
constraint_algorithm= lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 20 fs, largely irrelevant with Verlet
scheme
rcoulomb= 1.0   ; short-range electrostatic cutoff
(in nm)
rvdw= 1.0   ; short-range van der Waals cutoff
(in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for
long-range electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more
accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; Pressure coupling on
in NPT
pcoupltype  = isotropic ; uniform scaling of
box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure,
in bar
compressibility = 4.5e-5; isothermal compressibility of
water, bar^-1
refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off







*;simulated annealingannealing= single
periodicannealing-npoints  = 4 3annealing-time= 0 4000 8000 12000 16000
2 24000annealing-temp   = 300 310 315 330 320 310 300*
when I executed the mdrun with above .mdp file I got following error.



*Fatal error:First time point for annealing > init_t.  *
Kindly tell me what could be the reason for the error.


Probably because you're starting from a previous run (continuation = 
yes), grompp is taking the initial time frame as the one found in the 
checkpoint file, so you can't start your annealing from t = 0 in that case.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Average and bfactors.pdb

[Justin Lemkul]

On 8/20/17 11:48 PM, farial tavakoli wrote:

  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear justin
Thank you for your replyIt means, there is no problem, i can ignore it ang go 
ahead?


Sure, but keep in mind that this "average structure" has no physical 
meaning.  The B-factors are (possibly) useful, but also keep in mind 
that solution dynamics and crystal dynamics are very different, so 
comparing the two may or may not be useful.


-Justin

Sent from Yahoo Mail for iPhone


On Monday, August 21, 2017, 2:34 AM, Justin Lemkul  wrote:



On 8/20/17 11:51 AM, farial tavakoli wrote:

   blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gmx users
I removed jumps from my .xtc file before by using gmx trjconv and viewed my 
complex in vmd, it was ok and rhere was no jump. Now i use gmx rmsf and the 
same .xtc file which was created after using gmx trjconv, but when i view 
average. Pdb and bfactors.pdb files in pymol, my protein is still brocken. 
Would you please advice me how to solve this problem?

There is no physical significance to an average set of coordinates.  These may
appear broken or distorted.

http://www.gromacs.org/Documentation/Terminology/Average_Structure

-Justin



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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[gmx-users] Fwd: Question on gmx_wham with two reaction coordinates.

[Yuanchao Liu (MSU)]

Hi all

Sorry to post this again. I will appreciate if anybody can help with this

I have a question on dealing with two reaction coordinates by gmx_wham. I
did umbrella sampling on glucose 6-phosphate molecule on a poly-Lys peptide
surface. Because the peptide is neither cylindrical nor spherical
symmetric, I have to restraint each window around a specific point, using
two reaction coordinates (distance and direction). As results, the ligand's
trajectory looks pretty well. It was restraint around a specific points,
instead of going around a sphere surface when I used 'distance' alone.

However, I got some issue using WHAM for analysis. That is, GROMACS seems
not to allow me to use WHAM with two pull geometry (distance and
direction). So I have to pick only one reaction coordinate to do the
analysis. When I run regular wham, I got this issue:

Fatal error:

umbrella0.tpr: Your pull coordinates have different pull geometry
(coordinate

1: distance, coordinate 2: direction)

If you want to use only some pull coordinates in WHAM, please select them
with

option gmx wham -is


I refer this link to pick one of the two reaction coordiantes to work on
WHAM.
https://urldefense.proofpoint.com/v2/url?u=http-3A__manual.gromacs.org_documentation_2016_onlinehelp_gmx-2Dwham.html&d=DwIFaQ&c=nE__W8dFE-shTxStwXtp0A&r=gCy395jfSTIKIGBjdJ8SwSg8yN7wywRqF0ilx8ZoefpMNPZKIUY0jXzHKcFUwcQV&m=erg0OZLT3d1xG1FDq6J357V6VeRaFwNylkFDDHWoibM&s=yaLzHjzylI66bC_grW7Y2MuN-XHXdno8fH3jtTGa5AI&e=
 

See all the figures in this link:
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.evernote.com_l_AAMsNYa6HXZFeqNDTbsiV4HO0ta2KY-2Dnz7s_&d=DwIFaQ&c=nE__W8dFE-shTxStwXtp0A&r=gCy395jfSTIKIGBjdJ8SwSg8yN7wywRqF0ilx8ZoefpMNPZKIUY0jXzHKcFUwcQV&m=erg0OZLT3d1xG1FDq6J357V6VeRaFwNylkFDDHWoibM&s=JmmnE853X5gvKEdb7Ru78xmCvsQ5foSjLDnAhhlitLY&e=
 

When I only selected 'distance' for WHAM, the histogram and PMF looks like
this (Figure 1). I can somewhat understand the insufficient overlap at
0.5-0.75 nm could result in some abnormal segment in PMF, but what really
confused me is the global decreasing on PMF. Then histogram looks just
right.

Here is the result when only selecting 'direction' as the reaction
coordinate for wham (Figure 2). Gromacs's WHAM still output the distance as
x-axis, and the histogram is different form the above one.

Then I just simply add these two PMFs together and got following plots.
(Figure 3) The summation looks like what I expected. I can not understand
this. Because the restraints by 'distance' and 'direction' are
perpendicular to each other, the coordinate-1's WHAM result should be
something like what I got from single reaction coordinate. I expected the
coordinate-1's WHAM result should look like the summation result. I do not
have experience on dealing with two reaction coordinates. So, I will
appreciate it if anybody has suggestions on how to figure this out.

Here is the pulling parameter for my umbrella sampling: Pull code

pull= yes
pull_ngroups= 2  ; there are two pulling groups
pull_ncoords= 2 ; two reaction coordiante to
restraint the molecule around its initial position
pull_group1_name= Other  ; ligand
pull_group2_name= ref_group  . reference group, it is a part of
my peptide
; first reaction coordinate
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2   ; two groups the pulling will be
applied
pull_coord1_dim = Y Y Y
pull_coord1_rate= 0.0  ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0
; second reaction coordinate
pull_coord2_type= umbrella  ; harmonic biasing force
pull_coord2_geometry= direction  ; simple distance increase
pull_coord2_vec  = 11.018  -20.969  13.824
pull_coord2_groups  = 1 2
pull_coord2_dim = Y Y Y
pull_coord2_rate= 0.0  ; 0.01 nm per ps = 10 nm per ns
pull_coord2_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord2_start   = yes   ; define initial COM distance > 0



Best

Yuanchao Liu (刘元超)
Ph.D. Candidate
Department of Chemical Engineering and Materials Science
428 South Shaw Lane, Room 3263
Michigan State University
East Lansing, Michigan 48824-4437

Email: ycliu1...@gmail.com; liuyu...@msu.edu; liuyu...@egr.msu.edu
Cell:+1 (517)-763-1806 <+1%20517-763-1806>
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Re: [gmx-users] MPICH2 error

[Souparno Adhikary]

Okay, it worked. After I put on -DCMAKE_C_COMPILER and -DCMAKE_CXX_COMPILER
in my configuration options. Thanks.

Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.

On Mon, Aug 21, 2017 at 5:04 PM, Mark Abraham 
wrote:

> Hi,
>
> Your previous report didn't use eg CMAKE_CXX_COMPILER=mpic++ etc
>
> This should set up the linking. Anyway, if you build the shared version and
> don't build the static version of mpich nothing can go wrong. But there's
> nothing for gromacs to do about it...
>
> Mark
>
> On Mon, 21 Aug 2017 13:10 Souparno Adhikary  wrote:
>
> > I am using MPI compilers to do the thing. I reinstalled MPICH2 using the
> > options and it looks the same. Sorry...
> >
> > Souparno Adhikary,
> > CHPC Lab,
> > Department of Microbiology,
> > University of Calcutta.
> >
> > On Mon, Aug 21, 2017 at 4:08 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Please use the MPI wrapper compilers provided by the MPI library to
> > compile
> > > programs that use that MPI library, as I suggested last time. Managing
> > this
> > > stuff is its job.
> > >
> > > Mark
> > >
> > > On Mon, Aug 21, 2017 at 12:34 PM Souparno Adhikary <
> > souparno...@gmail.com>
> > > wrote:
> > >
> > > > I am posting this error again. Please help. I installed mpich2 with
> > > > CXXFLAGS='-fPIC' and --enable-shared options.
> > > >
> > > > I configured gromacs with the following command:
> > > >
> > > > /root/cmake-3.9.1-Linux-x86_64/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON
> > > > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON
> > > > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.1.4
> > > >
> > > > After I ran make, I am getting the following error:
> > > >
> > > > /usr/bin/ld: /usr/local/lib/libmpich.a(allreduce.o): relocation
> > > R_X86_64_32
> > > > against `.rodata.str1.8' can not be used when making a shared object;
> > > > recompile with -fPIC
> > > > /usr/local/lib/libmpich.a: could not read symbols: Bad value
> > > > collect2: ld returned 1 exit status
> > > > make[2]: *** [lib/libgromacs_mpi.so.1.4.0] Error 1
> > > > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > > > make: *** [all] Error 2
> > > >
> > > > Can anyone please help???
> > > >
> > > > Souparno Adhikary,
> > > > CHPC Lab,
> > > > Department of Microbiology,
> > > > University of Calcutta.
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
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> > > > posting!
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> or
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> > > >
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Re: [gmx-users] MPICH2 error

[Mark Abraham]

Hi,

Your previous report didn't use eg CMAKE_CXX_COMPILER=mpic++ etc

This should set up the linking. Anyway, if you build the shared version and
don't build the static version of mpich nothing can go wrong. But there's
nothing for gromacs to do about it...

Mark

On Mon, 21 Aug 2017 13:10 Souparno Adhikary  wrote:

> I am using MPI compilers to do the thing. I reinstalled MPICH2 using the
> options and it looks the same. Sorry...
>
> Souparno Adhikary,
> CHPC Lab,
> Department of Microbiology,
> University of Calcutta.
>
> On Mon, Aug 21, 2017 at 4:08 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Please use the MPI wrapper compilers provided by the MPI library to
> compile
> > programs that use that MPI library, as I suggested last time. Managing
> this
> > stuff is its job.
> >
> > Mark
> >
> > On Mon, Aug 21, 2017 at 12:34 PM Souparno Adhikary <
> souparno...@gmail.com>
> > wrote:
> >
> > > I am posting this error again. Please help. I installed mpich2 with
> > > CXXFLAGS='-fPIC' and --enable-shared options.
> > >
> > > I configured gromacs with the following command:
> > >
> > > /root/cmake-3.9.1-Linux-x86_64/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON
> > > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON
> > > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.1.4
> > >
> > > After I ran make, I am getting the following error:
> > >
> > > /usr/bin/ld: /usr/local/lib/libmpich.a(allreduce.o): relocation
> > R_X86_64_32
> > > against `.rodata.str1.8' can not be used when making a shared object;
> > > recompile with -fPIC
> > > /usr/local/lib/libmpich.a: could not read symbols: Bad value
> > > collect2: ld returned 1 exit status
> > > make[2]: *** [lib/libgromacs_mpi.so.1.4.0] Error 1
> > > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > > make: *** [all] Error 2
> > >
> > > Can anyone please help???
> > >
> > > Souparno Adhikary,
> > > CHPC Lab,
> > > Department of Microbiology,
> > > University of Calcutta.
> > > --
> > > 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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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
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Re: [gmx-users] MPICH2 error

[Souparno Adhikary]

I am using MPI compilers to do the thing. I reinstalled MPICH2 using the
options and it looks the same. Sorry...

Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.

On Mon, Aug 21, 2017 at 4:08 PM, Mark Abraham 
wrote:

> Hi,
>
> Please use the MPI wrapper compilers provided by the MPI library to compile
> programs that use that MPI library, as I suggested last time. Managing this
> stuff is its job.
>
> Mark
>
> On Mon, Aug 21, 2017 at 12:34 PM Souparno Adhikary 
> wrote:
>
> > I am posting this error again. Please help. I installed mpich2 with
> > CXXFLAGS='-fPIC' and --enable-shared options.
> >
> > I configured gromacs with the following command:
> >
> > /root/cmake-3.9.1-Linux-x86_64/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON
> > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON
> > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.1.4
> >
> > After I ran make, I am getting the following error:
> >
> > /usr/bin/ld: /usr/local/lib/libmpich.a(allreduce.o): relocation
> R_X86_64_32
> > against `.rodata.str1.8' can not be used when making a shared object;
> > recompile with -fPIC
> > /usr/local/lib/libmpich.a: could not read symbols: Bad value
> > collect2: ld returned 1 exit status
> > make[2]: *** [lib/libgromacs_mpi.so.1.4.0] Error 1
> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > make: *** [all] Error 2
> >
> > Can anyone please help???
> >
> > Souparno Adhikary,
> > CHPC Lab,
> > Department of Microbiology,
> > University of Calcutta.
> > --
> > 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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[gmx-users] FEP calculations on multiple nodes

[Vikas Dubey]

Hi everyone,

I am trying runa  FEP calculation with a system of ~25 particles. I
have 20 windows and I am currently running my simulations on 1 node each.
Since, my system is big, I just get 2.5ns in day. So, I thought to run each
of my window on multiple nodes but for some reason, it crashes immediately
after starting with an error.


*Segmentation fault (core dumped)*

Simulations run smoothly on one node. No error there. I tried to see file
but there was nothing written there. Any help would be very much
appreciated.


Thanks,
Vikas
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Re: [gmx-users] MPICH2 error

[Mark Abraham]

Hi,

Please use the MPI wrapper compilers provided by the MPI library to compile
programs that use that MPI library, as I suggested last time. Managing this
stuff is its job.

Mark

On Mon, Aug 21, 2017 at 12:34 PM Souparno Adhikary 
wrote:

> I am posting this error again. Please help. I installed mpich2 with
> CXXFLAGS='-fPIC' and --enable-shared options.
>
> I configured gromacs with the following command:
>
> /root/cmake-3.9.1-Linux-x86_64/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON
> -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON
> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.1.4
>
> After I ran make, I am getting the following error:
>
> /usr/bin/ld: /usr/local/lib/libmpich.a(allreduce.o): relocation R_X86_64_32
> against `.rodata.str1.8' can not be used when making a shared object;
> recompile with -fPIC
> /usr/local/lib/libmpich.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[2]: *** [lib/libgromacs_mpi.so.1.4.0] Error 1
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
>
> Can anyone please help???
>
> Souparno Adhikary,
> CHPC Lab,
> Department of Microbiology,
> University of Calcutta.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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[gmx-users] MPICH2 error

[Souparno Adhikary]

I am posting this error again. Please help. I installed mpich2 with
CXXFLAGS='-fPIC' and --enable-shared options.

I configured gromacs with the following command:

/root/cmake-3.9.1-Linux-x86_64/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.1.4

After I ran make, I am getting the following error:

/usr/bin/ld: /usr/local/lib/libmpich.a(allreduce.o): relocation R_X86_64_32
against `.rodata.str1.8' can not be used when making a shared object;
recompile with -fPIC
/usr/local/lib/libmpich.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [lib/libgromacs_mpi.so.1.4.0] Error 1
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2

Can anyone please help???

Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.
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[gmx-users] Residue 1 mapping problem?

[morpheus]

Hi,

I would like to simulate chain D and E of pdb-id 1oga but pdb2gmx complains
about the first (?) residues of the 2 chains:

"WARNING: WARNING: Residue 1 named GLN of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed."

I assume it means this GLN (as it is the first residue of the file):

ATOM   3164  N   GLN D   3  22.890 -35.428 -11.393  1.00
22.91   N
ATOM   3165  CA  GLN D   3  21.681 -35.958 -10.698  1.00
21.34   C
ATOM   3166  C   GLN D   3  20.599 -36.345 -11.695  1.00
20.99   C
ATOM   3167  O   GLN D   3  20.336 -35.616 -12.646  1.00
22.83   O
ATOM   3168  CB  GLN D   3  21.091 -34.889  -9.797  1.00
20.05   C
ATOM   3169  CG  GLN D   3  21.926 -34.493  -8.608  1.00
20.82   C
ATOM   3170  CD  GLN D   3  21.388 -33.220  -8.008  1.00
19.14   C
ATOM   3171  OE1 GLN D   3  21.602 -32.139  -8.553  1.00
21.07   O
ATOM   3172  NE2 GLN D   3  20.653 -33.341  -6.916  1.00
21.18   N
ATOM   3173  N   LEU D   4  19.949 -37.480 -11.445  1.00
21.46   N
ATOM   3174  CA  LEU D   4  18.889 -37.992 -12.300  1.00
22.61   C
ATOM   3175  C   LEU D   4  17.679 -38.428 -11.487  1.00
20.04   C
ATOM   3176  O   LEU D   4  17.814 -38.838 -10.337  1.00
21.78   O
ATOM   3177  CB  LEU D   4  19.386 -39.229 -13.059  1.00
22.96   C
ATOM   3178  CG  LEU D   4  20.637 -39.103 -13.912  1.00
26.17   C
ATOM   3179  CD1 LEU D   4  21.062 -40.497 -14.412  1.00
29.25   C
ATOM   3180  CD2 LEU D   4  20.341 -38.189 -15.071  1.00
27.56   C

Any ideas? My commands and gromacs output below.

Thanks!



[b@localhost newTry]$ gmx pdb2gmx -f JM22_fullMHC_fullTCR.pdb -o
JM22_fullMHC_fullTCR.gro -p JM22_fullMHC_fullTCR.top -i
JM22_fullMHC_fullTCR.posre.itp -ignh -vsite hydrogens
 :-) GROMACS - gmx pdb2gmx, 2016.2 (-:

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

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Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
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check out http://www.gromacs.org for more information.

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GROMACS:  gmx pdb2gmx, version 2016.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Working dir:
/home/b/data/projects/anton_mutationsMHC/complexes_withConstTcrRegions/JM22_onlyTCR/newTry
Command line:
  gmx pdb2gmx -f JM22_fullMHC_fullTCR.pdb -o JM22_fullMHC_fullTCR.gro -p
JM22_fullMHC_fullTCR.top -i JM22_fullMHC_fullTCR.posre.itp -ignh -vsite
hydrogens


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

Using the Gromos53a6 force field in directory gromos53a6.ff

Opening force field file
/usr/share/gromacs/top/gromos5