[gmx-users] Pro-lig under one molecule type

[Sana Saeed]

hi i am working of protein ligand binding free energy calculation, i have seen 
some tutorials, like from alchemistry websites and from some paper works. i 
made ligand topology with acpype (amber.ff) and used pdb2gmx for protein 
topology, then i combined gro files to make a complex. now i dont know how to 
make complex topology. i already studies and used tutorials from Bevanlab but 
it doesnt provide info about how to include protein and ligand as one 
moleculetype. and also how should i get the dihedral, angle and distance 
restraints. i studied gromacs manual about this but it doesnt provide any 
direction. if anyone have some tutorial, kindly suggest. Thanks in advance

 ; distance restraints[ bonds ];    i     j  type     r0A     r1A     r2A    
fcA    r0B     r1B     r2B    fcB  2143  1656    10     0.615   0.615   10.0   
0.0    0.615   0.615   10.0   4184.000
[ angle_restraints ];   ai    aj    ak    al  type    thA      fcA    multA  
thB      fcB    multB  1658  1656  2143  1656     1    92.14    0.0    1    
92.14    41.840    1  1656  2143  2142  2143     1    107.4    0.0    1    
107.4    41.840    1 [ dihedral_restraints ];   ai    aj    ak    al  type    
phiA     dphiA  fcA    phiB      dphiB  fcB  1668  1658  1656  2143     1    
157.05   0.0    0.0    157.05    0.0    41.840  1658  1656  2143  2142     1    
-129.56   0.0    0.0    -129.56    0.0    41.840  1656  2143  2142  2140     1  
  166.61   0.0    0.0    166.61    0.0    41.840




Sana Saeed Khan,Teaching-Research AssistantChemoinformatics LabGraduate 
Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, 
South Korea.
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[gmx-users] Problem in Potential energy of protein after energy minimization

[Subhashree Rout]

Hii

I am simulating protein (PfCDPK5) in water. After performing energy
minimization, the potential energy of my protein is 2.86082e+07. As
mentioned in the tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html,
the Epot should be negative.

The em.mdp file-
; minim.mdp - used as input into grompp to generate em.tpr
integrator= steep; Algorithm (steep = steepest descent
minimization)
emtol= 1000.0  ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps= 5  ; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list
and long range forces
cutoff-scheme   = Verlet
ns_type= grid; Method to determine neighbor list
(simple, grid)
coulombtype= PME; Treatment of long range electrostatic
interactions
rcoulomb= 1.0; Short-range electrostatic cut-off
rvdw= 1.0; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

Kindly suggest where I am going wrong.
-- 
Subhashree Rout
PhD Scholar
Bioinformatics Lab
KIIT School of Biotechnology
KIIT University
Bhubaneswar
Odisha
INDIA
Pin-751024
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Re: [gmx-users] tip4p2005 with gromacs 4.6.5

[Irem Altan]

Thanks! It solved most of the problem.
I am now getting an error during energy minimization:

The [molecules] section of your topology specifies more than one block of
a [moleculetype] with a [settles] block. Only one such is allowed. If you
are trying to partition your solvent into different *groups* (e.g. for
freezing, T-coupling, etc.) then you are using the wrong approach. Index
files specify groups. Otherwise, you may wish to change the least-used
block of molecules with SETTLE constraints into 3 normal constraints.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I am in fact labeling water molecules separately, but this had worked before 
with TIP4P.

my topology file looks like this:

; Include forcefield parameters
#include "./amber99sb.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_B.itp"
#include "topol_Other_chain_A2.itp"
#include "topol_Other_chain_B2.itp"

; Include water topology
#include "./amber99sb.ff/tip4p2005.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct  fcxfcyfcz
   11 10001000   1000
#endif

; Include topology for ions
#include "./amber99sb.ff/ions.itp"
#include "./tip4p2005cw.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
Other_chain_A2  1
Other_chain_B2  1
HO496
HO462
SOL 5763
NA   6
CL   10

where tip4p2005cw.itp has the molecule name defined as HO4:

[ moleculetype ]
; molnamenrexcl
  HO42

Does this somehow clash with TIP4P’s HO4? Do I need to name it differently?

Best,
Irem
On Feb 17, 2016, at 5:48 PM, Justin Lemkul 
> wrote:



On 2/17/16 5:41 PM, Irem Altan wrote:
Hi,

I would like to use TIP4P2005 with Gromacs 4.6.5 for a protein simulation with 
water. I have the .itp and .gro files for the model.
I am using a slightly modified version of the Amber forcefields, so I have a 
folder called amber99sb.ff in my working directory. I have added a file called 
tip4p2005.itp into that folder. I then tried the following:

pdb2gmx -f amber99sb.ff/ -water tip4p2005.itp -o box.gro -p topol.top

as well as

pdb2gmx -f amber99sb.ff/ -water tip4p2005 -o box.gro -p topol.top

both of which result in an error saying “invalid argument tip4p2005(.itp) for 
option -water”.

How can I get this to work?


It must match the first field of an entry in watermodels.dat in the force field 
directory.

Also note that pdb2gmx -f takes a coordinate file, not a directory name.  That 
will cause a whole host of failures...

-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] tip4p2005 with gromacs 4.6.5

[Justin Lemkul]

On 2/17/16 5:41 PM, Irem Altan wrote:

Hi,

I would like to use TIP4P2005 with Gromacs 4.6.5 for a protein simulation with 
water. I have the .itp and .gro files for the model.
I am using a slightly modified version of the Amber forcefields, so I have a 
folder called amber99sb.ff in my working directory. I have added a file called 
tip4p2005.itp into that folder. I then tried the following:

pdb2gmx -f amber99sb.ff/ -water tip4p2005.itp -o box.gro -p topol.top

as well as

pdb2gmx -f amber99sb.ff/ -water tip4p2005 -o box.gro -p topol.top

both of which result in an error saying “invalid argument tip4p2005(.itp) for 
option -water”.

How can I get this to work?



It must match the first field of an entry in watermodels.dat in the force field 
directory.


Also note that pdb2gmx -f takes a coordinate file, not a directory name.  That 
will cause a whole host of failures...


-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] Unknown bond_atomtype

[Nash, Anthony]

Thanks Justin,

I think that¹s everything I need to know.

Kind regards
Anthony

Dr Anthony Nash
Department of Chemistry
University College London





On 17/02/2016 22:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Justin Lemkul"
 wrote:

>
>
>On 2/17/16 5:11 PM, Nash, Anthony wrote:
>> Hi,
>>
>> Thanks for the information, Mark. I fully parameterised the bonded terms
>> using QM data and some software I wrote. Now that I¹ve sorted out
>> ffnonbonded [atomtypes], all that remains are some missing angle terms.
>>I
>> want to have the forcefield files correct so an MD simulation can be
>> generated with very little changes to the topol file after running
>> pdb2gmx. I do have a couple of questions that I hope you could help me
>> with.
>>
>> 1) For grompp to compile successfully, must every molecule/residue have
>>a
>> complete set of dihedral angle force constants?
>
>grompp will complain about any missing parameters, triggering a failure.
>
>> 2) It appears as though the residue to residue bond connectivity in my
>> force field files aren¹t correctly parameterised. In NGLY-MOD-CGLY, a
>> bonded term is added to the topol for the C in NGLY to the N in CGLY. To
>> avoid this must I add an entry such as -C N in the [ bonds ] section of
>> the [ MOD1 ] residue definition in aminoacids.rtp? I¹m unsure what ³-C²
>> means.
>>
>
>- indicates an atom in the previous residue, + means in the next residue.
> So -C 
>is the C in the previous residue.  If you're getting bonds between NGLY
>and 
>CGLY, ignoring the intervening residue, you probably either haven't set
>your 
>modified residue as Protein in residuetypes.dat or it doesn't have a C
>(which it 
>should, if it's an amino acid.
>
>-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] Unknown bond_atomtype

[Justin Lemkul]

On 2/17/16 5:11 PM, Nash, Anthony wrote:

Hi,

Thanks for the information, Mark. I fully parameterised the bonded terms
using QM data and some software I wrote. Now that I’ve sorted out
ffnonbonded [atomtypes], all that remains are some missing angle terms. I
want to have the forcefield files correct so an MD simulation can be
generated with very little changes to the topol file after running
pdb2gmx. I do have a couple of questions that I hope you could help me
with.

1) For grompp to compile successfully, must every molecule/residue have a
complete set of dihedral angle force constants?


grompp will complain about any missing parameters, triggering a failure.


2) It appears as though the residue to residue bond connectivity in my
force field files aren’t correctly parameterised. In NGLY-MOD-CGLY, a
bonded term is added to the topol for the C in NGLY to the N in CGLY. To
avoid this must I add an entry such as -C N in the [ bonds ] section of
the [ MOD1 ] residue definition in aminoacids.rtp? I’m unsure what “-C”
means.



- indicates an atom in the previous residue, + means in the next residue.  So -C 
is the C in the previous residue.  If you're getting bonds between NGLY and 
CGLY, ignoring the intervening residue, you probably either haven't set your 
modified residue as Protein in residuetypes.dat or it doesn't have a C (which it 
should, if it's an amino acid.


-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] Unknown bond_atomtype

[Nash, Anthony]

Hi,

Thanks for the information, Mark. I fully parameterised the bonded terms
using QM data and some software I wrote. Now that I’ve sorted out
ffnonbonded [atomtypes], all that remains are some missing angle terms. I
want to have the forcefield files correct so an MD simulation can be
generated with very little changes to the topol file after running
pdb2gmx. I do have a couple of questions that I hope you could help me
with. 

1) For grompp to compile successfully, must every molecule/residue have a
complete set of dihedral angle force constants?
2) It appears as though the residue to residue bond connectivity in my
force field files aren’t correctly parameterised. In NGLY-MOD-CGLY, a
bonded term is added to the topol for the C in NGLY to the N in CGLY. To
avoid this must I add an entry such as -C N in the [ bonds ] section of
the [ MOD1 ] residue definition in aminoacids.rtp? I’m unsure what “-C”
means.

Thanks for all your help.

Anthony


Dr Anthony Nash
Department of Chemistry
University College London





On 17/02/2016 21:46, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Mark Abraham"  wrote:

>Hi,
>
>Your MOD residues are LYS connected by a ring, so the atom types and bonds
>sections should be pretty much as for LYS, with the ring parts perhaps
>along the lines of TYR. If you have done a full parameterization somehow
>and have specialized atom types, then yes, those bonded and non-bonded
>parameters need to go into the databases for grompp to look up (or then
>can
>also go in the [bonds] section of the .rtp, I think).
>
>Mark
>
>On Wed, Feb 17, 2016 at 10:39 PM Nash, Anthony  wrote:
>
>>
>> Dear Mark,
>>
>>
>> I didn’t expect the problem was in ffnonbonded.itp. Problem solved.
>>Thanks
>> for the earlier hint.
>>
>> Anthony
>>
>> On 17/02/2016 18:01, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>>on
>> behalf of Nash, Anthony"
>> > a.n...@ucl.ac.uk> wrote:
>>
>> >Hi Mark,
>> >
>> >Further to my earlier email. I’ve answered the query as to whether atom
>> >types and names can be the same. This is fine, judging by The N N and
>>O O
>> >in all of the amino acid types.
>> >
>> >I suspect I either have an additional problem or I have identified the
>> >root cause of my original problem. Every non-terminal amino acid has a
>>-C
>> >N line in [ bonds ]. My custom residue does not. I assume this is to do
>> >with amino acid connectivity. How do I implement this single bond if I
>> >have the connectivity NGLY-MOD-CGLY, where EVERY atom in MOD is
>>completely
>> >new? I assume this is where you meant use existing types. So in theory
>>I
>> >could just change the very first atom of MOD, which would be MN1 to N,
>>and
>> >then go into ffbonded and just change MN1-MC1 to N-MC1 for the first
>>bond
>> >parameter the MOD residue.
>> >
>> >Apologies for rambling on, I *think* I know what I am doing.
>> >
>> >Thanks
>> >Anthony
>> >
>> >Dr Anthony Nash
>> >Department of Chemistry
>> >University College London
>> >
>> >
>> >
>> >
>> >
>> >On 17/02/2016 17:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>> on
>> >behalf of Nash, Anthony"
>> >> >a.n...@ucl.ac.uk> wrote:
>> >
>> >>Hi Mark,
>> >>
>> >>Thanks for the reply. I’m a little confused when you say “Choose
>>existing
>> >>types”. Are you saying that I am confined to only those atom types
>>that
>> >>come along with the forcefield upon installation, or that I can add
>>new
>> >>types but I’ve made a slight mishap between when specifying them
>>within
>> >>the [atom] section of my new residue?
>> >>
>> >>Also, I am guessing there is no issue with atom NAME and TYPE being
>> >>identical?
>> >>
>> >>Many thanks
>> >>Anthony
>> >>
>> >>Dr Anthony Nash
>> >>Department of Chemistry
>> >>University College London
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>On 17/02/2016 16:43,
>>"gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>> >>on
>> >>behalf of Mark Abraham"
>> >>> >>on behalf of mark.j.abra...@gmail.com> wrote:
>> >>
>> >>>Hi,
>> >>>
>> >>>You've specified a type for your atom in [atoms] and elsewhere a bond
>> >>>that
>> >>>uses it. Grompp has to find parameters for a bond between those two
>> >>>types,
>> >>>etc. Choose existing types ;-)
>> >>>
>> >>>Mark
>> >>>
>> >>>On Wed, 17 Feb 2016 17:27 Nash, Anthony  wrote:
>> >>>
>>  Hi all,
>> 
>>  As per a previous email (cross linking two peptide chains), I¹ve
>> created a
>>  brand new crosslink (think disulphide bond) residue from scratch. I
>> have
>>  defined it in all the files necessary (.rtp, residuetypes,
>>specbond,
>>  atomtypes, ffbonded, ffnonbonded) and it has got past pdb2gmx with
>>no
>>  problems.
>> 
>>  Unfortunately when I run 

Re: [gmx-users] Unknown bond_atomtype

[Mark Abraham]

Hi,

Your MOD residues are LYS connected by a ring, so the atom types and bonds
sections should be pretty much as for LYS, with the ring parts perhaps
along the lines of TYR. If you have done a full parameterization somehow
and have specialized atom types, then yes, those bonded and non-bonded
parameters need to go into the databases for grompp to look up (or then can
also go in the [bonds] section of the .rtp, I think).

Mark

On Wed, Feb 17, 2016 at 10:39 PM Nash, Anthony  wrote:

>
> Dear Mark,
>
>
> I didn’t expect the problem was in ffnonbonded.itp. Problem solved. Thanks
> for the earlier hint.
>
> Anthony
>
> On 17/02/2016 18:01, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
> behalf of Nash, Anthony"
>  a.n...@ucl.ac.uk> wrote:
>
> >Hi Mark,
> >
> >Further to my earlier email. I’ve answered the query as to whether atom
> >types and names can be the same. This is fine, judging by The N N and O O
> >in all of the amino acid types.
> >
> >I suspect I either have an additional problem or I have identified the
> >root cause of my original problem. Every non-terminal amino acid has a -C
> >N line in [ bonds ]. My custom residue does not. I assume this is to do
> >with amino acid connectivity. How do I implement this single bond if I
> >have the connectivity NGLY-MOD-CGLY, where EVERY atom in MOD is completely
> >new? I assume this is where you meant use existing types. So in theory I
> >could just change the very first atom of MOD, which would be MN1 to N, and
> >then go into ffbonded and just change MN1-MC1 to N-MC1 for the first bond
> >parameter the MOD residue.
> >
> >Apologies for rambling on, I *think* I know what I am doing.
> >
> >Thanks
> >Anthony
> >
> >Dr Anthony Nash
> >Department of Chemistry
> >University College London
> >
> >
> >
> >
> >
> >On 17/02/2016 17:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> on
> >behalf of Nash, Anthony"
> > >a.n...@ucl.ac.uk> wrote:
> >
> >>Hi Mark,
> >>
> >>Thanks for the reply. I’m a little confused when you say “Choose existing
> >>types”. Are you saying that I am confined to only those atom types that
> >>come along with the forcefield upon installation, or that I can add new
> >>types but I’ve made a slight mishap between when specifying them within
> >>the [atom] section of my new residue?
> >>
> >>Also, I am guessing there is no issue with atom NAME and TYPE being
> >>identical?
> >>
> >>Many thanks
> >>Anthony
> >>
> >>Dr Anthony Nash
> >>Department of Chemistry
> >>University College London
> >>
> >>
> >>
> >>
> >>
> >>On 17/02/2016 16:43, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> >>on
> >>behalf of Mark Abraham"
> >> >>on behalf of mark.j.abra...@gmail.com> wrote:
> >>
> >>>Hi,
> >>>
> >>>You've specified a type for your atom in [atoms] and elsewhere a bond
> >>>that
> >>>uses it. Grompp has to find parameters for a bond between those two
> >>>types,
> >>>etc. Choose existing types ;-)
> >>>
> >>>Mark
> >>>
> >>>On Wed, 17 Feb 2016 17:27 Nash, Anthony  wrote:
> >>>
>  Hi all,
> 
>  As per a previous email (cross linking two peptide chains), I¹ve
> created a
>  brand new crosslink (think disulphide bond) residue from scratch. I
> have
>  defined it in all the files necessary (.rtp, residuetypes, specbond,
>  atomtypes, ffbonded, ffnonbonded) and it has got past pdb2gmx with no
>  problems.
> 
>  Unfortunately when I run grompp (5.0.4) I get the following error:
> 
>  Fatal error:
>  Unknown bond_atomtype MN1 <‹‹ first atom in my new residue
> 
> 
>  At first I thought my topology might be pointing to the wrong
> forcefield,
>  but I¹ve checked and double checked:
> 
>  #include
> "/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp"
>  #include "modic.itp"
>  ;#ifdef POSRES
>  ;#include "posre.itp"
>  ;#endif
> 
>  [ system ]
>  ; Name
>  MODIC with glycine terminal ends
> 
>  [ molecules ]
>  ; Compound#mols
>  MODIC 1
> 
> 
>  I¹m going to take a guess at what the problem is. Each of the atoms in
> the
>  residue was derived from scratch.Therefore, they have a completely new
>  type. I wasn¹t feeling very creative with my naming convention so the
> atom
>  name and the atom type are identical e.g.,
> 
>  ;MODIC crosslink
>  [ MOD1 ]
>   [ atoms ]
>  ; NAMETYPECHARGE  NUMBER
>  MN1 MN1 -0.3640 1
>  MC1 MC1 0.0358  2
>  MC15MC150.4871  3
>  Š
> 
>  Š
> 
>  Will this have confused grompp?
> 
>  Many thanks
>  Anthony
> 
>  Dr Anthony Nash
>  Department of Chemistry
>  

Re: [gmx-users] Unknown bond_atomtype

[Nash, Anthony]

Dear Mark,


I didn’t expect the problem was in ffnonbonded.itp. Problem solved. Thanks
for the earlier hint.

Anthony

On 17/02/2016 18:01, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Nash, Anthony"
 wrote:

>Hi Mark,
>
>Further to my earlier email. I’ve answered the query as to whether atom
>types and names can be the same. This is fine, judging by The N N and O O
>in all of the amino acid types.
>
>I suspect I either have an additional problem or I have identified the
>root cause of my original problem. Every non-terminal amino acid has a -C
>N line in [ bonds ]. My custom residue does not. I assume this is to do
>with amino acid connectivity. How do I implement this single bond if I
>have the connectivity NGLY-MOD-CGLY, where EVERY atom in MOD is completely
>new? I assume this is where you meant use existing types. So in theory I
>could just change the very first atom of MOD, which would be MN1 to N, and
>then go into ffbonded and just change MN1-MC1 to N-MC1 for the first bond
>parameter the MOD residue.
>
>Apologies for rambling on, I *think* I know what I am doing.
>
>Thanks
>Anthony
>
>Dr Anthony Nash
>Department of Chemistry
>University College London
>
>
>
>
>
>On 17/02/2016 17:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
>behalf of Nash, Anthony"
>a.n...@ucl.ac.uk> wrote:
>
>>Hi Mark,
>>
>>Thanks for the reply. I’m a little confused when you say “Choose existing
>>types”. Are you saying that I am confined to only those atom types that
>>come along with the forcefield upon installation, or that I can add new
>>types but I’ve made a slight mishap between when specifying them within
>>the [atom] section of my new residue?
>>
>>Also, I am guessing there is no issue with atom NAME and TYPE being
>>identical?
>>
>>Many thanks
>>Anthony
>>
>>Dr Anthony Nash
>>Department of Chemistry
>>University College London
>>
>>
>>
>>
>>
>>On 17/02/2016 16:43, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>>on
>>behalf of Mark Abraham"
>>>on behalf of mark.j.abra...@gmail.com> wrote:
>>
>>>Hi,
>>>
>>>You've specified a type for your atom in [atoms] and elsewhere a bond
>>>that
>>>uses it. Grompp has to find parameters for a bond between those two
>>>types,
>>>etc. Choose existing types ;-)
>>>
>>>Mark
>>>
>>>On Wed, 17 Feb 2016 17:27 Nash, Anthony  wrote:
>>>
 Hi all,

 As per a previous email (cross linking two peptide chains), I¹ve
created a
 brand new crosslink (think disulphide bond) residue from scratch. I
have
 defined it in all the files necessary (.rtp, residuetypes, specbond,
 atomtypes, ffbonded, ffnonbonded) and it has got past pdb2gmx with no
 problems.

 Unfortunately when I run grompp (5.0.4) I get the following error:

 Fatal error:
 Unknown bond_atomtype MN1 <‹‹ first atom in my new residue


 At first I thought my topology might be pointing to the wrong
forcefield,
 but I¹ve checked and double checked:

 #include 
"/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp"
 #include "modic.itp"
 ;#ifdef POSRES
 ;#include "posre.itp"
 ;#endif

 [ system ]
 ; Name
 MODIC with glycine terminal ends

 [ molecules ]
 ; Compound#mols
 MODIC 1


 I¹m going to take a guess at what the problem is. Each of the atoms in
the
 residue was derived from scratch.Therefore, they have a completely new
 type. I wasn¹t feeling very creative with my naming convention so the
atom
 name and the atom type are identical e.g.,

 ;MODIC crosslink
 [ MOD1 ]
  [ atoms ]
 ; NAMETYPECHARGE  NUMBER
 MN1 MN1 -0.3640 1
 MC1 MC1 0.0358  2
 MC15MC150.4871  3
 Š

 Š

 Will this have confused grompp?

 Many thanks
 Anthony

 Dr Anthony Nash
 Department of Chemistry
 University College London



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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] Unknown bond_atomtype

[Nash, Anthony]

Hi Mark,

Further to my earlier email. I’ve answered the query as to whether atom
types and names can be the same. This is fine, judging by The N N and O O
in all of the amino acid types.

I suspect I either have an additional problem or I have identified the
root cause of my original problem. Every non-terminal amino acid has a -C
N line in [ bonds ]. My custom residue does not. I assume this is to do
with amino acid connectivity. How do I implement this single bond if I
have the connectivity NGLY-MOD-CGLY, where EVERY atom in MOD is completely
new? I assume this is where you meant use existing types. So in theory I
could just change the very first atom of MOD, which would be MN1 to N, and
then go into ffbonded and just change MN1-MC1 to N-MC1 for the first bond
parameter the MOD residue.

Apologies for rambling on, I *think* I know what I am doing.

Thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London





On 17/02/2016 17:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Nash, Anthony"
 wrote:

>Hi Mark,
>
>Thanks for the reply. I’m a little confused when you say “Choose existing
>types”. Are you saying that I am confined to only those atom types that
>come along with the forcefield upon installation, or that I can add new
>types but I’ve made a slight mishap between when specifying them within
>the [atom] section of my new residue?
>
>Also, I am guessing there is no issue with atom NAME and TYPE being
>identical?
>
>Many thanks
>Anthony
>
>Dr Anthony Nash
>Department of Chemistry
>University College London
>
>
>
>
>
>On 17/02/2016 16:43, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
>behalf of Mark Abraham" on behalf of mark.j.abra...@gmail.com> wrote:
>
>>Hi,
>>
>>You've specified a type for your atom in [atoms] and elsewhere a bond
>>that
>>uses it. Grompp has to find parameters for a bond between those two
>>types,
>>etc. Choose existing types ;-)
>>
>>Mark
>>
>>On Wed, 17 Feb 2016 17:27 Nash, Anthony  wrote:
>>
>>> Hi all,
>>>
>>> As per a previous email (cross linking two peptide chains), I¹ve
>>>created a
>>> brand new crosslink (think disulphide bond) residue from scratch. I
>>>have
>>> defined it in all the files necessary (.rtp, residuetypes, specbond,
>>> atomtypes, ffbonded, ffnonbonded) and it has got past pdb2gmx with no
>>> problems.
>>>
>>> Unfortunately when I run grompp (5.0.4) I get the following error:
>>>
>>> Fatal error:
>>> Unknown bond_atomtype MN1 <‹‹ first atom in my new residue
>>>
>>>
>>> At first I thought my topology might be pointing to the wrong
>>>forcefield,
>>> but I¹ve checked and double checked:
>>>
>>> #include 
>>>"/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp"
>>> #include "modic.itp"
>>> ;#ifdef POSRES
>>> ;#include "posre.itp"
>>> ;#endif
>>>
>>> [ system ]
>>> ; Name
>>> MODIC with glycine terminal ends
>>>
>>> [ molecules ]
>>> ; Compound#mols
>>> MODIC 1
>>>
>>>
>>> I¹m going to take a guess at what the problem is. Each of the atoms in
>>>the
>>> residue was derived from scratch.Therefore, they have a completely new
>>> type. I wasn¹t feeling very creative with my naming convention so the
>>>atom
>>> name and the atom type are identical e.g.,
>>>
>>> ;MODIC crosslink
>>> [ MOD1 ]
>>>  [ atoms ]
>>> ; NAMETYPECHARGE  NUMBER
>>> MN1 MN1 -0.3640 1
>>> MC1 MC1 0.0358  2
>>> MC15MC150.4871  3
>>> Š
>>>
>>> Š
>>>
>>> Will this have confused grompp?
>>>
>>> Many thanks
>>> Anthony
>>>
>>> Dr Anthony Nash
>>> Department of Chemistry
>>> University College London
>>>
>>>
>>>
>>> --
>>> 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.
>>>
>>-- 
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>>posting!
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>
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Re: [gmx-users] Unknown bond_atomtype

[Nash, Anthony]

Hi Mark,

Thanks for the reply. I’m a little confused when you say “Choose existing
types”. Are you saying that I am confined to only those atom types that
come along with the forcefield upon installation, or that I can add new
types but I’ve made a slight mishap between when specifying them within
the [atom] section of my new residue?

Also, I am guessing there is no issue with atom NAME and TYPE being
identical?

Many thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London





On 17/02/2016 16:43, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Mark Abraham"  wrote:

>Hi,
>
>You've specified a type for your atom in [atoms] and elsewhere a bond that
>uses it. Grompp has to find parameters for a bond between those two types,
>etc. Choose existing types ;-)
>
>Mark
>
>On Wed, 17 Feb 2016 17:27 Nash, Anthony  wrote:
>
>> Hi all,
>>
>> As per a previous email (cross linking two peptide chains), I¹ve
>>created a
>> brand new crosslink (think disulphide bond) residue from scratch. I have
>> defined it in all the files necessary (.rtp, residuetypes, specbond,
>> atomtypes, ffbonded, ffnonbonded) and it has got past pdb2gmx with no
>> problems.
>>
>> Unfortunately when I run grompp (5.0.4) I get the following error:
>>
>> Fatal error:
>> Unknown bond_atomtype MN1 <‹‹ first atom in my new residue
>>
>>
>> At first I thought my topology might be pointing to the wrong
>>forcefield,
>> but I¹ve checked and double checked:
>>
>> #include 
>>"/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp"
>> #include "modic.itp"
>> ;#ifdef POSRES
>> ;#include "posre.itp"
>> ;#endif
>>
>> [ system ]
>> ; Name
>> MODIC with glycine terminal ends
>>
>> [ molecules ]
>> ; Compound#mols
>> MODIC 1
>>
>>
>> I¹m going to take a guess at what the problem is. Each of the atoms in
>>the
>> residue was derived from scratch.Therefore, they have a completely new
>> type. I wasn¹t feeling very creative with my naming convention so the
>>atom
>> name and the atom type are identical e.g.,
>>
>> ;MODIC crosslink
>> [ MOD1 ]
>>  [ atoms ]
>> ; NAMETYPECHARGE  NUMBER
>> MN1 MN1 -0.3640 1
>> MC1 MC1 0.0358  2
>> MC15MC150.4871  3
>> Š
>>
>> Š
>>
>> Will this have confused grompp?
>>
>> Many thanks
>> Anthony
>>
>> Dr Anthony Nash
>> Department of Chemistry
>> University College London
>>
>>
>>
>> --
>> 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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>
>* 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] correct rlist and Verlet scheme

[Szilárd Páll]

As soon as I sent this off I realized that the work you refer to is
probably the one that was done by/at DE Shaw, so they must have used
Desmond so the non-bonded treatment is not exactly as in AMBER, but my
point is still valid regarding trying to reproduce the pair list
buffer.

--
Szilárd

On Wed, Feb 17, 2016 at 6:07 PM, Szilárd Páll  wrote:
> Hi,
>
> The short-range interaction treatment in AMBER and GROMACS is quite
> different (to the best of my knowledge), so obsessing about rlist
> seems pointless to me.
>
> AMBER uses a heuristic list update where search is triggered based
> particles tracking ("safe" but inefficient strategy), whereas GROMACS
> uses a fixed list update frequency. The automated buffer estimate that
> ensures control of the non-boneded drift. Without controlling _both_
> buffer and search frequency (and a bunch of other subtle
> implementation details) you won't achieve identical computation.
>
> Hence, if you want to have (more or less) the same non-bonded
> calculation implemented in GROMACS, strictly speaking you'd have to
> use nstlist=1 or if you accept to be a bit less strict, a huge manual
> buffer (and small-ish nstlist) should achieve more or less the same.
> However, there are plenty of other algorithmic and implementation
> differences between AMBER and GROMACS, so I don't think it's worth
> worrying about getting the Verlet list buffer length to match.
>
> Cheers,
> --
> Szilárd
>
> PS: I thought AMBER FF was parametrized with 0.9 nm cut-off, isn't it?
>
>
> On Wed, Feb 17, 2016 at 2:45 PM, Mark Abraham  
> wrote:
>> Hi,
>>
>> Yes, what you say is true, but very much "in short" and AFAIK true of all
>> MD packages. :-)
>>
>> If e.g. AMBER (or anyone else) has a test suite for any force field, then
>> we'll seriously consider implementing it, to e.g. verify before each
>> release. :-) IMO, defining such a suite is a research topic itself -
>> particularly as the original parameterizations did so in the context of
>> limitations in the methods of the day. If a force field was parameterized
>> with a fixed buffer because nobody then knew how large a buffer was
>> necessary for a given quality of relevant observable, it does not follow
>> that the only possible acceptable practice now is to use that fixed buffer.
>>
>> Similar considerations apply to things like e.g. the use of long-ranged
>> corrections for dispersion interactions. e.g. AMBER99 was parameterized
>> without such corrections, so probably has built into its parameters some
>> compensating errors, and any kind of validation-by-replication should in
>> principle not use such corrections. But these days, I think that nobody
>> would actually recommend parameterizing a force field without something
>> like that, and experience suggests that using one is an improvement, even
>> if though the change is not officially sanctioned anywhere that I know of.
>> IMO showing that some range of force fields shows satisfactory agreement
>> with experiment under certain .mdp setting combinations is useful evidence
>> of an implementation that is valid, and that is what one can see in the
>> literature.
>>
>> The state of the art in software engineering is that nobody much has time
>> to test all the things that they'd like to test. (One large exception is
>> software for control of devices that potentially affect human health.)
>> Scientific software development has additional challenges because the
>> people doing it are often lacking in formal training in best practice, and
>> have to appear to publish science, in order to keep attracting funding, and
>> this directly conflicts with spending time on good software engineering
>> practice that granting and tenure committees will ignore later in their
>> careers...
>>
>> Mark
>>
>> On Wed, Feb 17, 2016 at 1:01 PM Timofey Tyugashev 
>> wrote:
>>
>>> In short, FFs were tested to some degree when they were added in GROMACS
>>> to reproduce AMBER results, but there is no certainty if they actually
>>> do this now and 'correct' mdp settings to run them are unknown. For any
>>> of the versions that are listed in GROMACS.
>>> Is that correct, or I'm missing something in translation?
>>>
>>> 16.02.2016 18:03, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:
>>> > Message: 2
>>> > Date: Tue, 16 Feb 2016 11:23:06 +
>>> > From: Mark Abraham
>>> > To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se
>>> > Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue
>>> >   76
>>> > Message-ID:
>>> >   <
>>> camnumasutdhr8sot1qt4xdczogsdjsfgo8umiuhrpffxxfa...@mail.gmail.com>
>>> > Content-Type: text/plain; charset=UTF-8
>>> >
>>> > Hi,
>>> >
>>> > The ports of all the AMBER force fields were all tested to reproduce
>>> AMBER
>>> > when when they were added to GROMACS. Many of our regressiontests use
>>> those
>>> > force fields, so there is 

Re: [gmx-users] gmx chi output clarification

[Francesco Carbone]

thank you Justin,
kind as always!
I hope that David (or who knows gmx chi better) will have a look at this
post soon.

In the meanwhile I'll use gmx chi (5.0.4), having care of keeping an eye on
the results , and comparing them with other source.

Regards,

Francesco

On 17 February 2016 at 12:49, Justin Lemkul  wrote:

>
>
> On 2/17/16 7:11 AM, Francesco Carbone wrote:
>
>> Thank you Justin,
>>
>> I'm not a pro in C, but I think that in the code, the omega angle is
>> defined as CA-C-N-CA (Bug #953 discussed this)
>> ...
>> dl[i].j0[edOmega] = n/4;
>> id[n++] = dl[i].atm.minCalpha;
>> id[n++] = dl[i].atm.minCalpha;
>> id[n++] = dl[i].atm.N;
>> id[n++] = dl[i].atm.Cn[1];
>> ...
>>
>> I then calculated the same angle using gmx chi (5.0.4) , g_chi (4.6), gmx
>> angle (5.0.4) and pdbtorsion (an in house tool that is always right ,of
>> course this is what my supervisor says :D)
>>
>> If I use pdbs dumped from a trajectory, all of them provides similar
>> values
>> (3-4-0.2-1).
>> On the other hand, if I'm using a pdb coming from outside source (
>> rcsb.org),
>> gmx chi is the only one that gives "flipped" values.
>> If I remove the flip (173 -180° ) I obtain a plausible value, but then why
>> don't I see this "flip" when I use "gmx chi" with a trajectory or a pdb
>> dumped from the trajectory?
>>
>>
> Hopefully whoever wrote the code (David?) will comment, as this is the
> extent of what I know about gmx chi (since I haven't used it in a long
> time).
>
> -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
>
> ==
> --
> Gromacs Users mailing list
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> posting!
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Re: [gmx-users] Unknown bond_atomtype

[Mark Abraham]

Hi,

You've specified a type for your atom in [atoms] and elsewhere a bond that
uses it. Grompp has to find parameters for a bond between those two types,
etc. Choose existing types ;-)

Mark

On Wed, 17 Feb 2016 17:27 Nash, Anthony  wrote:

> Hi all,
>
> As per a previous email (cross linking two peptide chains), I¹ve created a
> brand new crosslink (think disulphide bond) residue from scratch. I have
> defined it in all the files necessary (.rtp, residuetypes, specbond,
> atomtypes, ffbonded, ffnonbonded) and it has got past pdb2gmx with no
> problems.
>
> Unfortunately when I run grompp (5.0.4) I get the following error:
>
> Fatal error:
> Unknown bond_atomtype MN1 <‹‹ first atom in my new residue
>
>
> At first I thought my topology might be pointing to the wrong forcefield,
> but I¹ve checked and double checked:
>
> #include "/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp"
> #include "modic.itp"
> ;#ifdef POSRES
> ;#include "posre.itp"
> ;#endif
>
> [ system ]
> ; Name
> MODIC with glycine terminal ends
>
> [ molecules ]
> ; Compound#mols
> MODIC 1
>
>
> I¹m going to take a guess at what the problem is. Each of the atoms in the
> residue was derived from scratch.Therefore, they have a completely new
> type. I wasn¹t feeling very creative with my naming convention so the atom
> name and the atom type are identical e.g.,
>
> ;MODIC crosslink
> [ MOD1 ]
>  [ atoms ]
> ; NAMETYPECHARGE  NUMBER
> MN1 MN1 -0.3640 1
> MC1 MC1 0.0358  2
> MC15MC150.4871  3
> Š
>
> Š
>
> Will this have confused grompp?
>
> Many thanks
> Anthony
>
> Dr Anthony Nash
> Department of Chemistry
> University College London
>
>
>
> --
> 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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[gmx-users] Unknown bond_atomtype

[Nash, Anthony]

Hi all,

As per a previous email (cross linking two peptide chains), I¹ve created a
brand new crosslink (think disulphide bond) residue from scratch. I have
defined it in all the files necessary (.rtp, residuetypes, specbond,
atomtypes, ffbonded, ffnonbonded) and it has got past pdb2gmx with no
problems.  

Unfortunately when I run grompp (5.0.4) I get the following error:

Fatal error:
Unknown bond_atomtype MN1 <‹‹ first atom in my new residue


At first I thought my topology might be pointing to the wrong forcefield,
but I¹ve checked and double checked:

#include "/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp"
#include "modic.itp"
;#ifdef POSRES
;#include "posre.itp"
;#endif

[ system ]
; Name
MODIC with glycine terminal ends

[ molecules ]
; Compound#mols
MODIC 1


I¹m going to take a guess at what the problem is. Each of the atoms in the
residue was derived from scratch.Therefore, they have a completely new
type. I wasn¹t feeling very creative with my naming convention so the atom
name and the atom type are identical e.g.,

;MODIC crosslink
[ MOD1 ]
 [ atoms ]
; NAMETYPECHARGE  NUMBER
MN1 MN1 -0.3640 1
MC1 MC1 0.0358  2
MC15MC150.4871  3
Š

Š

Will this have confused grompp?

Many thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London



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Re: [gmx-users] NPT equilibration with small cell

[Tsjerk Wassenaar]

Hey :)

Since pressure is so ill-defined at those volumes, you may as well run NVT
then at a more or less plausible volume. That will relieve the worry that
the deviations from the intended physics (in light of the force field
chosen) will cause the system to expand or contract out of control and you
can cherish some hope that the aberrations in the interactions sort of
balance. Of course, part of that should later be corrected by DFT geometry
optimization. As for the question which volume you need to use then, I can
only say that there is no answer. There is a distribution of possible
volumes for a small system at a given temperature. That is also true for
big systems, but there the distribution is much sharper.

Hope it helps,

Tsjerk

On Wed, Feb 17, 2016 at 1:47 PM, André Farias de Moura 
wrote:

> maybe just a historical curiosity, but small systems with only 100
> molecules or so and cutoffs of 0.7 nm were considered as best practices,
> maybe even state-of-art, in computer simulations of liquids:
>
> J. Chem. Phys. 79, 926 (1983); http://dx.doi.org/10.1063/1.445869
>
> nowadays you have to use systems like those for your AIMD for the same
> reasons they had too back in the day: not enough computer power to treat
> the system of the size you would like to.
>
> so I would do just like Vitaly suggested: classical MD with small
> system/small cutoffs, DFT geometry optimization and then your goal, the
> AIMD simulation.
>
> Andre
>
> On Wed, Feb 17, 2016 at 9:44 AM, VITALY V. CHABAN 
> wrote:
>
> > you are on the right way.
> >
> > set high pressure.
> >
> > set cut-offs to half box side.
> >
> > run classical MD, ~10 000 steps, and, afterwards, manually increase the
> box
> > sides to mimic the experimental density
> >
> > in the plane-wave DFT, run local optimization prior to AIMD.
> >
> >
> >
> >
> >
> >
> >
> >
> > On Tue, Feb 16, 2016 at 4:01 PM, Miguel Caro 
> wrote:
> >
> > > Hello,
> > >
> > > I was wondering if there is any reason why one should expect a constant
> > > pressure simulation not to work for a small cell. I am running a very
> > small
> > > cell (1.2 nm^3) simulation because I need it as input for ab initio
> MD. I
> > > am trying to simulate NPT at 1 atm and it seems like my cell, a mixture
> > of
> > > water and methanol, is expanding uncontrollably (to 10 nm^3).
> > >
> > > Is it not possible to do NPT for cells this small? I should add that
> NVT
> > > seems to work just fine for the same system.
> > >
> > > These are the settings I am using for the pressure coupling:
> > >
> > > Pcoupl = MTTK
> > > tau_p = 0.2
> > > compressibility = 4.5e-5
> > > ref_p = 1.0
> > >
> > > I have tried to do the same simulation with a supercell made up of
> 2x2x2
> > > periodic copies of my small cell and that seems to work fine. For that
> > > simulation, the only difference besides the cell size was the neighbors
> > > cutoffs, which I could increase from rlist = rcoulomb = 0.45, rvdw =
> 0.5
> > > for the small cell to rlist = rcoulomb = 0.8, rvdw = 1.1 for the
> > supercell.
> > > For the small cell the cutoff radii are rather limited by the box size.
> > >
> > > Thanks in advance,
> > > Miguel
> > >
> > > --
> > > *Dr. Miguel Caro*
> > > /Postdoctoral researcher/
> > > Department of Electrical Engineering and Automation,
> > > and COMP Centre of Excellence in Computational Nanoscience
> > > Aalto University, Finland
> > > Personal email: *mcar...@gmail.com*
> > > Work: *miguel.c...@aalto.fi*
> > > Website: http://mcaroba.dyndns.org
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > 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.
> >
>
>
>
> --
> _
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
-- 
Gromacs 

Re: [gmx-users] gmx chi output clarification

[Justin Lemkul]

On 2/17/16 7:11 AM, Francesco Carbone wrote:

Thank you Justin,

I'm not a pro in C, but I think that in the code, the omega angle is
defined as CA-C-N-CA (Bug #953 discussed this)
...
dl[i].j0[edOmega] = n/4;
id[n++] = dl[i].atm.minCalpha;
id[n++] = dl[i].atm.minCalpha;
id[n++] = dl[i].atm.N;
id[n++] = dl[i].atm.Cn[1];
...

I then calculated the same angle using gmx chi (5.0.4) , g_chi (4.6), gmx
angle (5.0.4) and pdbtorsion (an in house tool that is always right ,of
course this is what my supervisor says :D)

If I use pdbs dumped from a trajectory, all of them provides similar values
(3-4-0.2-1).
On the other hand, if I'm using a pdb coming from outside source (rcsb.org),
gmx chi is the only one that gives "flipped" values.
If I remove the flip (173 -180° ) I obtain a plausible value, but then why
don't I see this "flip" when I use "gmx chi" with a trajectory or a pdb
dumped from the trajectory?



Hopefully whoever wrote the code (David?) will comment, as this is the extent of 
what I know about gmx chi (since I haven't used it in a long time).


-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] NPT equilibration with small cell

[André Farias de Moura]

maybe just a historical curiosity, but small systems with only 100
molecules or so and cutoffs of 0.7 nm were considered as best practices,
maybe even state-of-art, in computer simulations of liquids:

J. Chem. Phys. 79, 926 (1983); http://dx.doi.org/10.1063/1.445869

nowadays you have to use systems like those for your AIMD for the same
reasons they had too back in the day: not enough computer power to treat
the system of the size you would like to.

so I would do just like Vitaly suggested: classical MD with small
system/small cutoffs, DFT geometry optimization and then your goal, the
AIMD simulation.

Andre

On Wed, Feb 17, 2016 at 9:44 AM, VITALY V. CHABAN 
wrote:

> you are on the right way.
>
> set high pressure.
>
> set cut-offs to half box side.
>
> run classical MD, ~10 000 steps, and, afterwards, manually increase the box
> sides to mimic the experimental density
>
> in the plane-wave DFT, run local optimization prior to AIMD.
>
>
>
>
>
>
>
>
> On Tue, Feb 16, 2016 at 4:01 PM, Miguel Caro  wrote:
>
> > Hello,
> >
> > I was wondering if there is any reason why one should expect a constant
> > pressure simulation not to work for a small cell. I am running a very
> small
> > cell (1.2 nm^3) simulation because I need it as input for ab initio MD. I
> > am trying to simulate NPT at 1 atm and it seems like my cell, a mixture
> of
> > water and methanol, is expanding uncontrollably (to 10 nm^3).
> >
> > Is it not possible to do NPT for cells this small? I should add that NVT
> > seems to work just fine for the same system.
> >
> > These are the settings I am using for the pressure coupling:
> >
> > Pcoupl = MTTK
> > tau_p = 0.2
> > compressibility = 4.5e-5
> > ref_p = 1.0
> >
> > I have tried to do the same simulation with a supercell made up of 2x2x2
> > periodic copies of my small cell and that seems to work fine. For that
> > simulation, the only difference besides the cell size was the neighbors
> > cutoffs, which I could increase from rlist = rcoulomb = 0.45, rvdw = 0.5
> > for the small cell to rlist = rcoulomb = 0.8, rvdw = 1.1 for the
> supercell.
> > For the small cell the cutoff radii are rather limited by the box size.
> >
> > Thanks in advance,
> > Miguel
> >
> > --
> > *Dr. Miguel Caro*
> > /Postdoctoral researcher/
> > Department of Electrical Engineering and Automation,
> > and COMP Centre of Excellence in Computational Nanoscience
> > Aalto University, Finland
> > Personal email: *mcar...@gmail.com*
> > Work: *miguel.c...@aalto.fi*
> > Website: http://mcaroba.dyndns.org
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> 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.
>



-- 
_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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Re: [gmx-users] gmx chi output clarification

[Francesco Carbone]

Thank you Justin,

I'm not a pro in C, but I think that in the code, the omega angle is
defined as CA-C-N-CA (Bug #953 discussed this)
...
dl[i].j0[edOmega] = n/4;
id[n++] = dl[i].atm.minCalpha;
id[n++] = dl[i].atm.minCalpha;
id[n++] = dl[i].atm.N;
id[n++] = dl[i].atm.Cn[1];
...

I then calculated the same angle using gmx chi (5.0.4) , g_chi (4.6), gmx
angle (5.0.4) and pdbtorsion (an in house tool that is always right ,of
course this is what my supervisor says :D)

If I use pdbs dumped from a trajectory, all of them provides similar values
(3-4-0.2-1).
On the other hand, if I'm using a pdb coming from outside source (rcsb.org),
gmx chi is the only one that gives "flipped" values.
If I remove the flip (173 -180° ) I obtain a plausible value, but then why
don't I see this "flip" when I use "gmx chi" with a trajectory or a pdb
dumped from the trajectory?

Regards,

Francesco



On 16 February 2016 at 17:53, Justin Lemkul  wrote:

>
>
> On 2/16/16 12:40 PM, Francesco Carbone wrote:
>
>> Thank you again for the quick response,
>>
>> I read that, but I'm calculating the omega angle which shouldn't be
>> affected that how phi and psi are calculated.
>>
>>
> http://skryb.info/m/gmx-us...@gromacs.org/438c0b56.4020...@xray.bmc.uu.se
>
> Looks like omega here is calculated as O-C-N-CA, not CA-C-N-CA.  Check the
> code to be sure.
>
> Furthermore, if I'm wrong, -1° it's not simply "usually small" different
>> than 173°.
>>
>>
> It is if the convention is flipped and 173 actually indicates -7.
>
> Clearly the gmx chi help info needs some more work.
>
>
> -Justin
>
> Regards,
>>
>> Francesco
>>
>>
>> On 16 February 2016 at 17:30, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 2/16/16 12:26 PM, Francesco Carbone wrote:
>>>
>>> Thank you Justin,

 I selected the atoms (CA-C-N-CA)  for the dihedral I want and check with
 "gmx angle" (gmx angle -f  -n ciao.ndx -type dihedral)

 If I use the trajectory (-f file.xtc and ndx from a gro file) I have a
 nice
 distribution around 0° (avrg -3°) , while if I use the original pdb (-f
 2bhl.pdb and ndx from pdb )  I have an average of -1°.
 These results seem plausible, but why is "gmx chi" giving completely
 different results when it checks the value in  a single structure?


  From the help info:
>>>
>>> * phi and psi dihedrals are calculated in a non-standard way, using
>>> H-N-CA-C
>>>for phi instead of C(-)-N-CA-C, and N-CA-C-O for psi instead of
>>> N-CA-C-N(+).
>>>This causes (usually small) discrepancies with the output of other
>>> tools
>>>like gmx rama.
>>>
>>> So gmx chi is just using a different convention, one that you should be
>>> able to convert as needed.
>>>
>>> -Justin
>>>
>>>
>>> Regards,
>>>

 Francesco


 On 16 February 2016 at 16:10, Justin Lemkul  wrote:



> On 2/16/16 10:16 AM, Francesco Carbone wrote:
>
> good afternoon,
>
>>
>> I'm trying to study the values of the omega dihedral (peptide bond)
>> for
>> a
>> specific Proline in my protein.
>> This Proline is known to exists in both cis and trans conformation(cis
>> while binding).
>>
>> In the pdb I used as starting point for the simulation (2bhl.pdb) the
>> Proline (172) is in cis configuration.
>> This is confirmed both by the people who make the pdb and also by vmd
>> ("fix
>> cis peptide bond" tool) .
>>
>> If I run the command:
>> gmx chi -s simulation.tpr -f simulation.xtc -o output.xvg -g
>> logfile.log
>> -omega -all
>>
>> I can see that the Proline has values in the neighbourhood of 0° (
>> +-20°
>> ),
>> which is fine, being in cis.
>>
>> The problem is that if I try to calculate the same dihedral in the
>> original
>> structure (2bhl.pdb), using:
>> gmx chi -s 2bhl_fixed.pdb -f 2bhl_fixed.pdb -o output.xvg -g
>> logfile.log
>> -omega -all
>> or
>> gmx chi -s 2bhl_fixed.pdb -f file.xtc -o output.xvg -g logfile.log
>> -omega
>> -all
>>
>> I obtain values close to 180°,suggesting that  the Proline is in
>> trans.
>>
>> How is it possible?
>>
>>
>> IIRC gmx chi does not use H atoms in the calculations of these
> dihedrals.
> Confirm with gmx angle -type dihedral that everything checks out.
>
> -Justin
>
>
> I also tried to set -ramomega, but I don't see any xpm file being
>
>> created.
>>
>> Am I doing something wrong?
>>
>> Regards,
>>
>> Francesco
>>
>>
>> --
>>
> ==
>
> 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

Re: [gmx-users] correct rlist and Verlet scheme

[Timofey Tyugashev]

In short, FFs were tested to some degree when they were added in GROMACS 
to reproduce AMBER results, but there is no certainty if they actually 
do this now and 'correct' mdp settings to run them are unknown. For any 
of the versions that are listed in GROMACS.

Is that correct, or I'm missing something in translation?

16.02.2016 18:03, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 2
Date: Tue, 16 Feb 2016 11:23:06 +
From: Mark Abraham
To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue
76
Message-ID:

Content-Type: text/plain; charset=UTF-8

Hi,

The ports of all the AMBER force fields were all tested to reproduce AMBER
when when they were added to GROMACS. Many of our regressiontests use those
force fields, so there is reason to expect that they all continue to work.
The Verlet scheme is tested to implement what the documentation says it
does. There have been bugs introduced (and fixed) in how GROMACS
preprocessing tools implement the requirements of AMBER force fields,
including ILDN.

To be able to say "this force field is tested to work correctly with this
cutoff scheme in this version of GROMACS" requires the community to agree
on what that means, e.g. a large collection of single-point energies+forces
agree to within a certain precision, and simulations done in a particular
model physics produce these ensembles with these observables, etc. That
hasn't happened yet. As far as I know, the ability of the different AMBER
code versions to correctly continue to implement all the AMBER force fields
has a similar kind of question mark over it. Just having the same name is
not enough;-)

Mark

On Tue, Feb 16, 2016 at 11:17 AM Timofey Tyugashev
wrote:


>So, are there any other Amber force fields more suitable and more tested
>for GROMACS?
>
>15.02.2016 21:00,gromacs.org_gmx-users-requ...@maillist.sys.kth.se  ?:

> >Message: 1
> >Date: Mon, 15 Feb 2016 13:15:02 +
> >From: Mark Abraham
> >To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se
> >Subject: Re: [gmx-users] correct rlist and Verlet scheme
> >Message-ID:
> >   <

>camnumatmbmgvbfj49ez+4k_bftdmkyfyiw5iz-eecwicujb...@mail.gmail.com>

> >Content-Type: text/plain; charset=UTF-8
> >
> >Hi,
> >
> >On Mon, Feb 15, 2016 at 12:17 PM Timofey Tyugashev<

>tyugas...@niboch.nsc.ru>

> >wrote:
> >

> >> >I've studied the relevant sections of the manual, but I don't consider
> >> >myself to be familiar enough with this field to successfully guess the
> >> >right settings.
> >> >
> >> >ff99sb-ildn is included in the gromacs distribution, so shouldn?t be
> >> >there some recommended settings for it?

> >Ideally, yes. But nobody has made a particular effort for that

>combination.

> >
> >Or else how was it tested to run

> >> >properly?
> >> >

> >In principle, one would have to e.g. show that
> >https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/   can be

>replicated.

> >That's not a straightforward proposition...

>--
>Gromacs Users mailing list
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>posting!
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Re: [gmx-users] NPT equilibration with small cell

[VITALY V. CHABAN]

you are on the right way.

set high pressure.

set cut-offs to half box side.

run classical MD, ~10 000 steps, and, afterwards, manually increase the box
sides to mimic the experimental density

in the plane-wave DFT, run local optimization prior to AIMD.








On Tue, Feb 16, 2016 at 4:01 PM, Miguel Caro  wrote:

> Hello,
>
> I was wondering if there is any reason why one should expect a constant
> pressure simulation not to work for a small cell. I am running a very small
> cell (1.2 nm^3) simulation because I need it as input for ab initio MD. I
> am trying to simulate NPT at 1 atm and it seems like my cell, a mixture of
> water and methanol, is expanding uncontrollably (to 10 nm^3).
>
> Is it not possible to do NPT for cells this small? I should add that NVT
> seems to work just fine for the same system.
>
> These are the settings I am using for the pressure coupling:
>
> Pcoupl = MTTK
> tau_p = 0.2
> compressibility = 4.5e-5
> ref_p = 1.0
>
> I have tried to do the same simulation with a supercell made up of 2x2x2
> periodic copies of my small cell and that seems to work fine. For that
> simulation, the only difference besides the cell size was the neighbors
> cutoffs, which I could increase from rlist = rcoulomb = 0.45, rvdw = 0.5
> for the small cell to rlist = rcoulomb = 0.8, rvdw = 1.1 for the supercell.
> For the small cell the cutoff radii are rather limited by the box size.
>
> Thanks in advance,
> Miguel
>
> --
> *Dr. Miguel Caro*
> /Postdoctoral researcher/
> Department of Electrical Engineering and Automation,
> and COMP Centre of Excellence in Computational Nanoscience
> Aalto University, Finland
> Personal email: *mcar...@gmail.com*
> Work: *miguel.c...@aalto.fi*
> Website: http://mcaroba.dyndns.org
> --
> Gromacs Users mailing list
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