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

Nash, Anthony a.nash at ucl.ac.uk
Wed Feb 24 15:26:07 CET 2016

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?

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.


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).
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:

>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
>> 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
>> 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
>> 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.
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