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

Nash, Anthony a.nash at ucl.ac.uk
Thu Feb 25 16:10:56 CET 2016 

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-bounces at maillist.sys.kth.se on
behalf of Mark Abraham" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se
on behalf of mark.j.abraham at gmail.com> wrote:

>Hi,
>
>On Wed, Feb 24, 2016 at 4:00 PM Nash, Anthony <a.nash at ucl.ac.uk> 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-bounces at maillist.sys.kth.se
>>on
>> behalf of Mark Abraham"
>><gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>> on behalf of mark.j.abraham at gmail.com> wrote:
>>
>> >Hi,
>> >
>> >On Wed, Feb 24, 2016 at 3:26 PM Nash, Anthony <a.nash at ucl.ac.uk> 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
>> >>NHCCOHHHHH
>> >> (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)   =  1.00000e+01
>> >>    Number of steps    =       200000
>> >>
>> >>
>> >> 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   31.4    0.1014   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-bounces at maillist.sys.kth.se
>> >>on
>> >> behalf of Mark Abraham"
>> >><gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>> >> on behalf of mark.j.abraham at gmail.com> wrote:
>> >>
>> >> >Hi,
>> >> >
>> >> >On Tue, Feb 23, 2016 at 11:03 AM Nash, Anthony <a.nash at ucl.ac.uk>
>> >>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
>> >> >--
>> >> >Gromacs Users mailing list
>> >> >
>> >> >* Please search the archive at
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>> >> >posting!
>> >> >
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>>or
>> >> >send a mail to gmx-users-request at gromacs.org.
>> >>
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