Re: [gmx-users] generating an initial structure with a gromacs compatible tool

[Nash, Anthony]

Hi Mark,

I’ve double checked and triple checked the output from Avogadro. It does
appear (within the constraints of my version and installation) that
resaving an already correct .pdb format will shift the X coordinate left
by one space. I’ve reported this issue.

Thank you for that information regarding the “renumbering”, this should
save me a lot of time.

With regards to my original problem, I fixed it this morning. I took your
recommendation to triple the atom ordering in my new residue and that’s
when I noticed the awful mistake! Rather than using the atom names in the
[ bonds ] entry of aminoacids.rtp, I had used their atom index within the
residue. Suffice to say grompp continued to work, but when I corrected
this mistake I immediately noticed an additional 50 bonds had been
processed by grompp. I’ve performed em, NVT and NPT. My structure is very
stable :) 

Many thanks for helping me trouble shoot.

Anthony




On 25/02/2016 13:12, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Mark Abraham"  wrote:

>Hi,
>
>On Wed, Feb 24, 2016 at 4:00 PM Nash, Anthony  wrote:
>
>> Hi Mark,
>>
>> I’m afraid I am not sure what you mean by your final point "Thus,
>>avoiding
>> the issue by not doing reordering.”
>>
>> I don’t think I’ve been as clear as I could have been, sorry about
>>that. I
>> am only using avogadro to attach the two glycine residues, NGLY and CGLY
>> to the backbone of my brand new fragment whose geometry comes from the
>> output of a HF/6-31G(p) optimisation. I load the Gaussian .pdb into
>> avogadro, attach the two glycine residues, and then resave without
>> disturbing the coordinates of the original fragment (of which the eq
>>bond
>> length and angles are based on). Unfortunately, going back to my
>>original
>> question of “does gromacs have its own editing tool”, avogadro adjusts
>>the
>> formats of the original Gaussian .pdb file (including deviating the
>> X-coordinate entry by a single character shift to the left, causing
>> pdb2gmx to throw out a warning for every atom in the system)
>
>
>That sounds like a bug in Avogadro, and you should complain about it. pdb
>is a fixed-column format.
>
>
>> plus puts in
>> the terminal glycines at the end of the file. This is no good as
>>pdb2gmx’s
>> understanding of amber requires the termini of each chain to be defined
>>by
>> the presence of NGLY-FRAGMENT-GCLY.
>>
>
>But this has a trivial fix just copy the NGLY fragment and put it at
>the start. The numbering doesn't matter, so long as the numbers do change
>"reasonably."
>
>Either way, I’ve successfully walked through the complete steps of
>> Gaussian optimisation and RESP derivation to a running NPT gromacs
>> simulation for an almost identical peptide residue. The fact that the
>> second one isn’t working is probably indicative of my atom ordering
>>being
>> skewered - perhaps by just two atoms!
>>
>
>Well, make a vacuum system with just ngly-fragment-cgly and do gmx dump on
>the .tpr. There's no docs on how that format works, but you can see what
>grompp has made of your topology, which can function as that "second pair
>of eyes." Just be alert that all the indexing in the dump starts from 0
>(because that's convenient in C programs).
>
>Mark
>
>Thanks
>> Anthony
>>
>> Dr Anthony Nash
>> Department of Chemistry
>> University College London
>>
>>
>>
>>
>>
>> On 24/02/2016 14:33, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>>on
>> behalf of Mark Abraham"
>>> on behalf of mark.j.abra...@gmail.com> wrote:
>>
>> >Hi,
>> >
>> >On Wed, Feb 24, 2016 at 3:26 PM Nash, Anthony  wrote:
>> >
>> >> Hi Mark,
>> >>
>> >> When you generate a peptide sequences in Avogadro the atom name
>>order in
>> >> the .pdb for NGLY (which is just GLY and required renaming) is
>> >>NHCCOH
>> >> (if my memory serves me right - ignore the shortening of the names),
>> >> whilst in the .rtp file of amberffsb.99 it is NHHHCHHCO. I’ve always
>> >> reordered by hand. You mention that atom order isn’t significant
>>until
>> >> grompp, are you suggesting the pdb2gmx will understand *any* order of
>> >> atoms within a residue?
>> >>
>> >
>> >Try it :-) You have a working case, so swap the order of the atoms in
>>the
>> >pdb2gmx input coordinate file, and re-run your scripts.
>> >
>> >With regards to your point about constraints - yes, you are right. I’m
>> >> using an energy minimisation .mdp input file without any mention of
>> >> constraints. I’ve never once had to do this within an energy
>> >>minimisation
>> >> (I must have very fortunate starting structures up until yesterday)
>> >>until
>> >> I come to use NVT and/or NPT steeping. I’ve just put on LINCS and
>>reran
>> >> the energy minimiation, see below for the output:
>> >>
>> >
>> >You aren't going to be able to use what Avogadro produces without
>> >understanding 

Re: [gmx-users] generating an initial structure with a gromacs compatible tool

[Mark Abraham]

Hi,

On Wed, Feb 24, 2016 at 4:00 PM Nash, Anthony  wrote:

> Hi Mark,
>
> I’m afraid I am not sure what you mean by your final point "Thus, avoiding
> the issue by not doing reordering.”
>
> I don’t think I’ve been as clear as I could have been, sorry about that. I
> am only using avogadro to attach the two glycine residues, NGLY and CGLY
> to the backbone of my brand new fragment whose geometry comes from the
> output of a HF/6-31G(p) optimisation. I load the Gaussian .pdb into
> avogadro, attach the two glycine residues, and then resave without
> disturbing the coordinates of the original fragment (of which the eq bond
> length and angles are based on). Unfortunately, going back to my original
> question of “does gromacs have its own editing tool”, avogadro adjusts the
> formats of the original Gaussian .pdb file (including deviating the
> X-coordinate entry by a single character shift to the left, causing
> pdb2gmx to throw out a warning for every atom in the system)


That sounds like a bug in Avogadro, and you should complain about it. pdb
is a fixed-column format.


> plus puts in
> the terminal glycines at the end of the file. This is no good as pdb2gmx’s
> understanding of amber requires the termini of each chain to be defined by
> the presence of NGLY-FRAGMENT-GCLY.
>

But this has a trivial fix just copy the NGLY fragment and put it at
the start. The numbering doesn't matter, so long as the numbers do change
"reasonably."

Either way, I’ve successfully walked through the complete steps of
> Gaussian optimisation and RESP derivation to a running NPT gromacs
> simulation for an almost identical peptide residue. The fact that the
> second one isn’t working is probably indicative of my atom ordering being
> skewered - perhaps by just two atoms!
>

Well, make a vacuum system with just ngly-fragment-cgly and do gmx dump on
the .tpr. There's no docs on how that format works, but you can see what
grompp has made of your topology, which can function as that "second pair
of eyes." Just be alert that all the indexing in the dump starts from 0
(because that's convenient in C programs).

Mark

Thanks
> Anthony
>
> Dr Anthony Nash
> Department of Chemistry
> University College London
>
>
>
>
>
> On 24/02/2016 14:33, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
> behalf of Mark Abraham"  on behalf of mark.j.abra...@gmail.com> wrote:
>
> >Hi,
> >
> >On Wed, Feb 24, 2016 at 3:26 PM Nash, Anthony  wrote:
> >
> >> Hi Mark,
> >>
> >> When you generate a peptide sequences in Avogadro the atom name order in
> >> the .pdb for NGLY (which is just GLY and required renaming) is
> >>NHCCOH
> >> (if my memory serves me right - ignore the shortening of the names),
> >> whilst in the .rtp file of amberffsb.99 it is NHHHCHHCO. I’ve always
> >> reordered by hand. You mention that atom order isn’t significant until
> >> grompp, are you suggesting the pdb2gmx will understand *any* order of
> >> atoms within a residue?
> >>
> >
> >Try it :-) You have a working case, so swap the order of the atoms in the
> >pdb2gmx input coordinate file, and re-run your scripts.
> >
> >With regards to your point about constraints - yes, you are right. I’m
> >> using an energy minimisation .mdp input file without any mention of
> >> constraints. I’ve never once had to do this within an energy
> >>minimisation
> >> (I must have very fortunate starting structures up until yesterday)
> >>until
> >> I come to use NVT and/or NPT steeping. I’ve just put on LINCS and reran
> >> the energy minimiation, see below for the output:
> >>
> >
> >You aren't going to be able to use what Avogadro produces without
> >understanding what it is producing. Just turning on constraints isn't
> >going
> >to result in a valid model if it was "parameterized" for something else.
> >Clearly the output coordinate file is not very close to the constrained
> >geometry, but you need to understand why that is before you know how to
> >handle it.
> >
> >
> >> Regarding the atom ordering - this is something I suspect, but I’ve
> >> trawled through every gromacs file I’ve changed, and input geometry and
> >>it
> >> all seems to be aligned. I suspect I need a fresh set of eyes.
> >>
> >
> >Thus, avoiding the issue by not doing reordering.
> >
> >Mark
> >
> >
> >> Thanks
> >> Anthony
> >>
> >>
> >> --
> >> Steepest Descents:
> >>Tolerance (Fmax)   =  1.0e+01
> >>Number of steps=   20
> >>
> >>
> >> Step 40, time 0.04 (ps)  LINCS WARNING
> >> relative constraint deviation after LINCS:
> >> rms 0.007405, max 0.034928 (between atoms 73 and 75)
> >> bonds that rotated more than 30 degrees:
> >>  atom 1 atom 2  angle  previous, current, constraint length
> >>  71 72   31.40.1014   0.1006  0.1010
> >>
> >>
> >> Energy minimization has stopped, but the forces have not converged to
> >>the
> >> 

Re: [gmx-users] generating an initial structure with a gromacs compatible tool

[Nash, Anthony]

Hi Mark,

I’m afraid I am not sure what you mean by your final point "Thus, avoiding
the issue by not doing reordering.”

I don’t think I’ve been as clear as I could have been, sorry about that. I
am only using avogadro to attach the two glycine residues, NGLY and CGLY
to the backbone of my brand new fragment whose geometry comes from the
output of a HF/6-31G(p) optimisation. I load the Gaussian .pdb into
avogadro, attach the two glycine residues, and then resave without
disturbing the coordinates of the original fragment (of which the eq bond
length and angles are based on). Unfortunately, going back to my original
question of “does gromacs have its own editing tool”, avogadro adjusts the
formats of the original Gaussian .pdb file (including deviating the
X-coordinate entry by a single character shift to the left, causing
pdb2gmx to throw out a warning for every atom in the system) plus puts in
the terminal glycines at the end of the file. This is no good as pdb2gmx’s
understanding of amber requires the termini of each chain to be defined by
the presence of NGLY-FRAGMENT-GCLY.

Either way, I’ve successfully walked through the complete steps of
Gaussian optimisation and RESP derivation to a running NPT gromacs
simulation for an almost identical peptide residue. The fact that the
second one isn’t working is probably indicative of my atom ordering being
skewered - perhaps by just two atoms!

Thanks
Anthony 

Dr Anthony Nash
Department of Chemistry
University College London





On 24/02/2016 14:33, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Mark Abraham"  wrote:

>Hi,
>
>On Wed, Feb 24, 2016 at 3:26 PM Nash, Anthony  wrote:
>
>> Hi Mark,
>>
>> When you generate a peptide sequences in Avogadro the atom name order in
>> the .pdb for NGLY (which is just GLY and required renaming) is
>>NHCCOH
>> (if my memory serves me right - ignore the shortening of the names),
>> whilst in the .rtp file of amberffsb.99 it is NHHHCHHCO. I’ve always
>> reordered by hand. You mention that atom order isn’t significant until
>> grompp, are you suggesting the pdb2gmx will understand *any* order of
>> atoms within a residue?
>>
>
>Try it :-) You have a working case, so swap the order of the atoms in the
>pdb2gmx input coordinate file, and re-run your scripts.
>
>With regards to your point about constraints - yes, you are right. I’m
>> using an energy minimisation .mdp input file without any mention of
>> constraints. I’ve never once had to do this within an energy
>>minimisation
>> (I must have very fortunate starting structures up until yesterday)
>>until
>> I come to use NVT and/or NPT steeping. I’ve just put on LINCS and reran
>> the energy minimiation, see below for the output:
>>
>
>You aren't going to be able to use what Avogadro produces without
>understanding what it is producing. Just turning on constraints isn't
>going
>to result in a valid model if it was "parameterized" for something else.
>Clearly the output coordinate file is not very close to the constrained
>geometry, but you need to understand why that is before you know how to
>handle it.
>
>
>> Regarding the atom ordering - this is something I suspect, but I’ve
>> trawled through every gromacs file I’ve changed, and input geometry and
>>it
>> all seems to be aligned. I suspect I need a fresh set of eyes.
>>
>
>Thus, avoiding the issue by not doing reordering.
>
>Mark
>
>
>> Thanks
>> Anthony
>>
>>
>> --
>> Steepest Descents:
>>Tolerance (Fmax)   =  1.0e+01
>>Number of steps=   20
>>
>>
>> Step 40, time 0.04 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.007405, max 0.034928 (between atoms 73 and 75)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>  71 72   31.40.1014   0.1006  0.1010
>>
>>
>> Energy minimization has stopped, but the forces have not converged to
>>the
>> requested precision Fmax < 10 (which may not be possible for your
>>system).
>> It
>> stopped because the algorithm tried to make a new step whose size was
>>too
>> small, or there was no change in the energy since last step. Either
>>way, we
>> regard the minimization as converged to within the available machine
>> precision, given your starting configuration and EM parameters.
>> You might need to increase your constraint accuracy, or turn
>> off constraints altogether (set constraints = none in mdp file)
>> ―
>>
>>
>>
>>
>>
>>
>> Dr Anthony Nash
>> Department of Chemistry
>> University College London
>>
>>
>>
>>
>>
>> On 24/02/2016 14:04, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>>on
>> behalf of Mark Abraham"
>>> on behalf of mark.j.abra...@gmail.com> wrote:
>>
>> >Hi,
>> >
>> >On Tue, Feb 23, 

Re: [gmx-users] generating an initial structure with a gromacs compatible tool

[Mark Abraham]

Hi,

On Wed, Feb 24, 2016 at 3:26 PM Nash, Anthony  wrote:

> Hi Mark,
>
> When you generate a peptide sequences in Avogadro the atom name order in
> the .pdb for NGLY (which is just GLY and required renaming) is NHCCOH
> (if my memory serves me right - ignore the shortening of the names),
> whilst in the .rtp file of amberffsb.99 it is NHHHCHHCO. I’ve always
> reordered by hand. You mention that atom order isn’t significant until
> grompp, are you suggesting the pdb2gmx will understand *any* order of
> atoms within a residue?
>

Try it :-) You have a working case, so swap the order of the atoms in the
pdb2gmx input coordinate file, and re-run your scripts.

With regards to your point about constraints - yes, you are right. I’m
> using an energy minimisation .mdp input file without any mention of
> constraints. I’ve never once had to do this within an energy minimisation
> (I must have very fortunate starting structures up until yesterday) until
> I come to use NVT and/or NPT steeping. I’ve just put on LINCS and reran
> the energy minimiation, see below for the output:
>

You aren't going to be able to use what Avogadro produces without
understanding what it is producing. Just turning on constraints isn't going
to result in a valid model if it was "parameterized" for something else.
Clearly the output coordinate file is not very close to the constrained
geometry, but you need to understand why that is before you know how to
handle it.


> Regarding the atom ordering - this is something I suspect, but I’ve
> trawled through every gromacs file I’ve changed, and input geometry and it
> all seems to be aligned. I suspect I need a fresh set of eyes.
>

Thus, avoiding the issue by not doing reordering.

Mark


> Thanks
> Anthony
>
>
> --
> Steepest Descents:
>Tolerance (Fmax)   =  1.0e+01
>Number of steps=   20
>
>
> Step 40, time 0.04 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.007405, max 0.034928 (between atoms 73 and 75)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>  71 72   31.40.1014   0.1006  0.1010
>
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 10 (which may not be possible for your system).
> It
> stopped because the algorithm tried to make a new step whose size was too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
> ―
>
>
>
>
>
>
> Dr Anthony Nash
> Department of Chemistry
> University College London
>
>
>
>
>
> On 24/02/2016 14:04, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
> behalf of Mark Abraham"  on behalf of mark.j.abra...@gmail.com> wrote:
>
> >Hi,
> >
> >On Tue, Feb 23, 2016 at 11:03 AM Nash, Anthony  wrote:
> >
> >> Hi all,
> >> Is there a friendly Gromacs compatible tool for generating a .gro/.pdb
> >> file using a specific forcefield topology specification within Gromacs
> >> itself? For context:
> >>
> >> I¹m in the process of fully parameterising five custom protein residues
> >> for the amber forcefield from ab initio calculations. Fragment #1 has
> >>been
> >> very successfully, with a production NPT simulation showing very little
> >> deviation from the equilibrium ab initio structure.
> >>
> >> Fragment #2, on the other hand, is driving me crazy. I derive partial
> >> charges, force constants, then I take the equilibrium structure, and
> >> replace the capped backbone ends (required for RESP) with NGLY and
> >>CGLY. I
> >> am using Avogadro to do this, which spits out a awful .pdb file which
> >> requires a lot of rearranging to be compatible with the atom order of
> >>the
> >> residues inside aminoacid.rtp in the amber99sb.ff.
> >
> >
> >But the .rtp entry is based on atom names. Atom order isn't significant
> >until grompp (and then it merely warns if the atom order of the input .gro
> >file does not match that of the .top). And you have an .rtp entry already,
> >what are you getting from Avogadro anyway?
> >
> >I hold the eq_structure
> >> fixed in avogadro and run an energy equilibrium over the new adjoining
> >> glycine residues. All appears fine, until I run a Gromacs energy
> >> minimisation. The entire customer residue expands gently (beyond the eq
> >> distances, by a few angstrom),
> >
> >
> >Clearly your energy minimization isn't using constraints. Should it? You
> >need to understand the basis under which Avogadro is parameterizing for
> >this force field...
> >
> >
> >> and then an NVT simulation throws out 

Re: [gmx-users] generating an initial structure with a gromacs compatible tool

[Nash, Anthony]

Hi Mark,

When you generate a peptide sequences in Avogadro the atom name order in
the .pdb for NGLY (which is just GLY and required renaming) is NHCCOH
(if my memory serves me right - ignore the shortening of the names),
whilst in the .rtp file of amberffsb.99 it is NHHHCHHCO. I’ve always
reordered by hand. You mention that atom order isn’t significant until
grompp, are you suggesting the pdb2gmx will understand *any* order of
atoms within a residue?

With regards to your point about constraints - yes, you are right. I’m
using an energy minimisation .mdp input file without any mention of
constraints. I’ve never once had to do this within an energy minimisation
(I must have very fortunate starting structures up until yesterday) until
I come to use NVT and/or NPT steeping. I’ve just put on LINCS and reran
the energy minimiation, see below for the output:

Regarding the atom ordering - this is something I suspect, but I’ve
trawled through every gromacs file I’ve changed, and input geometry and it
all seems to be aligned. I suspect I need a fresh set of eyes.

Thanks
Anthony 


--
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+01
   Number of steps=   20


Step 40, time 0.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007405, max 0.034928 (between atoms 73 and 75)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 71 72   31.40.1014   0.1006  0.1010


Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 10 (which may not be possible for your system).
It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)
―






Dr Anthony Nash
Department of Chemistry
University College London





On 24/02/2016 14:04, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Mark Abraham"  wrote:

>Hi,
>
>On Tue, Feb 23, 2016 at 11:03 AM Nash, Anthony  wrote:
>
>> Hi all,
>> Is there a friendly Gromacs compatible tool for generating a .gro/.pdb
>> file using a specific forcefield topology specification within Gromacs
>> itself? For context:
>>
>> I¹m in the process of fully parameterising five custom protein residues
>> for the amber forcefield from ab initio calculations. Fragment #1 has
>>been
>> very successfully, with a production NPT simulation showing very little
>> deviation from the equilibrium ab initio structure.
>>
>> Fragment #2, on the other hand, is driving me crazy. I derive partial
>> charges, force constants, then I take the equilibrium structure, and
>> replace the capped backbone ends (required for RESP) with NGLY and
>>CGLY. I
>> am using Avogadro to do this, which spits out a awful .pdb file which
>> requires a lot of rearranging to be compatible with the atom order of
>>the
>> residues inside aminoacid.rtp in the amber99sb.ff.
>
>
>But the .rtp entry is based on atom names. Atom order isn't significant
>until grompp (and then it merely warns if the atom order of the input .gro
>file does not match that of the .top). And you have an .rtp entry already,
>what are you getting from Avogadro anyway?
>
>I hold the eq_structure
>> fixed in avogadro and run an energy equilibrium over the new adjoining
>> glycine residues. All appears fine, until I run a Gromacs energy
>> minimisation. The entire customer residue expands gently (beyond the eq
>> distances, by a few angstrom),
>
>
>Clearly your energy minimization isn't using constraints. Should it? You
>need to understand the basis under which Avogadro is parameterizing for
>this force field...
>
>
>> and then an NVT simulation throws out a lot
>> of LINCS warnings.
>>
>> I am pretty confident that this is the fault of my initial structure, in
>> particular the angles (I¹m going to double check the FCs).
>
>
>The simplest explanation is that you are mangling the atom order so that
>the topology mdrun understands isn't the one you intend. But that comes
>down to what you have in your .rtp/.itp files.
>
>
>> But mean while
>> using Avogadro to build test structures is taking forever! Any
>> alternatives?
>
>
>acpype is popular conversion tool for AMBER topologies, I understand.
>
>Mark
>-- 
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[gmx-users] generating an initial structure with a gromacs compatible tool

[Nash, Anthony]

Hi all,
Is there a friendly Gromacs compatible tool for generating a .gro/.pdb
file using a specific forcefield topology specification within Gromacs
itself? For context:

I¹m in the process of fully parameterising five custom protein residues
for the amber forcefield from ab initio calculations. Fragment #1 has been
very successfully, with a production NPT simulation showing very little
deviation from the equilibrium ab initio structure.

Fragment #2, on the other hand, is driving me crazy. I derive partial
charges, force constants, then I take the equilibrium structure, and
replace the capped backbone ends (required for RESP) with NGLY and CGLY. I
am using Avogadro to do this, which spits out a awful .pdb file which
requires a lot of rearranging to be compatible with the atom order of the
residues inside aminoacid.rtp in the amber99sb.ff. I hold the eq_structure
fixed in avogadro and run an energy equilibrium over the new adjoining
glycine residues. All appears fine, until I run a Gromacs energy
minimisation. The entire customer residue expands gently (beyond the eq
distances, by a few angstrom), and then an NVT simulation throws out a lot
of LINCS warnings. 

I am pretty confident that this is the fault of my initial structure, in
particular the angles (I¹m going to double check the FCs). But mean while
using Avogadro to build test structures is taking forever! Any
alternatives?

Many thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London

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