[gmx-users] Re: \[gmx\-users\] The energy minimization\.\.\.\. (fwd)
TJ Piggot
t.piggot at bristol.ac.uk
Sat Aug 18 03:31:33 CEST 2007
Hi
Also please keep emails on the list, it helps everyone (you getting more
people's opinion than just mine, and people who may have a similar problem
in the future)
Tom
------------ Forwarded Message ------------
Date: 18 August 2007 02:29 +0100
From: TJ Piggot <t.piggot at bristol.ac.uk>
To: mjduan at smail.hust.edu.cn
Subject: Re: \[gmx\-users\] The energy minimization\.\.\.\.
Hi
I just quickly checked and your ATP pdb file works fine for me (it did have
some weird characters in it that i had to delete, not sure if this was
caused by pasting it into an email). I should point out that this pdb file
is incomplete as you are missing some hydrogen atoms (pdb2gmx should tell
you this if you modified your .rtp file correctly). See any of the GROMOS96
.rtp file ATP entries for the hydrogens you have missed that still are
included in a united atom ff.
Also your .mdp parameters work fine with your pdb file so i have no idea
what is going wrong when you try! Check you have modified the .rtp file
correctly and are supplying sensible commands to
pdb2gmx/editconf/grompp/mdrun are the last things i can suggest.
Good luck
Tom
--On 18 August 2007 08:17 +0800 MoJie Duan <mjduan at smail.hust.edu.cn> wrote:
> Hi,Tom:
> Thank you for your reply!
> Before the minimization, I just change the atoms name of ATP, so it can
> coordinated to the names in ffG43b1 (the atoms name of ATP in ffG43b1
> also changed, each atom have a three-letter name).
>
> My coordinate file (.pdb) was obtained from RCSB PDB, I extracted the xyz
> coordinates of ATP molecule from the a .pdb file of a protein, as
> following:
> _______________________________
> HETATM 7577 PG ATP 800 -4.997 4.425 -2.604 1.00
> 33.08 P
> HETATM 7578 O1G ATP 800 -5.685 5.603 -1.764 1.00
> 33.76 O
> HETATM 7579 O2G ATP 800 -3.427 4.765 -2.665 1.00 32.63
> 0; O
> HETATM 7580 O3G ATP 800 -5.273 3.100 -1.967 1.00
> 33.16 O
> HETATM 7581 PB ATP 800 -5.173 3.787 -5.388 1.00
> 34.37 P
> HETATM 7582 O1B ATP 800 -3.985 4.318 -6.120 1.00
> 33.33 O
> HETATM 7583 O2B ATP 800 -5.232 2.335 -5.045 1.00
> 33.33 O
> HETATM 7584 O3B ATP 800 -5.529 4.675 -4.089 1.00
> 33.22 O
> HETATM 7585 PA ATP 800 -7.773 3.348 -6.436 1.00
> 35.04 P
> HETATM 7586 O1A ATP 800 -8.260 2.720 -5.177 1.00
> 33.60 O
> HETATM 7587 O2A ATP 800 -7.501 2.503 -7.632 1.00
> 32.64 O
> HETATM 7588 O3A ATP 800 -6.483 4.274 -6.168 1.00
> 34.07 O
> HETATM 7589 O5' ATP 800 -8.787 4.518 0; -6.833 1.00
> 36.40 O
> HETATM 7590 C5' ATP 800 -8.403 5.464 -7.846 1.00
> 39.10 C
> HETATM 7591 C4' ATP 800 -9.604 6.315 -8.269 1.00
> 41.61 C
> HETATM 7592 O4' ATP 800 -10.793 5.471 -8.462 1.00
> 42.22 O
> HETATM 7593 C3' ATP 800 -9.937 7.303 -7.152 1.00
> 41.81 C
> HETATM 7594 O3' ATP 800 -10.228 8.5 59 -7.756 1.00
> 43.61 O
> HETATM 7595 C2' ATP 800 -11.191 6.724 -6.514 1.00
> 42.05 C
> HETATM 7596 O2' ATP 800 -12.023 7.764 -6.036 1.00
> 41.49 O
> HETATM 7597 C1' ATP 800 -11.875 6.025 -7.679 1.00
> 42.90 C
> HETATM 7598 N9 ATP 800 -12.608 4.832 -7.218 1.00
> 43.53 N
> HETATM 7599 C8 ATP 800 -12.077 3. 810 -6.547 1.00
> 43.35 C
> HETATM 7600 N7 ATP 800 -13.023 2.904 -6.309 1.00
> 44.02 N
> HETATM 7601 C5 ATP 800 -14.162 3.341 -6.835 1.00
> 44.22 C
> HETATM 7602 C6 ATP 800 -15.461 2.828 -6.899 1.00
> 44.02 C
> HETATM 7603 N6 ATP 800 -15.751 1.647 -6.351 1.00
> 43.35 N
> HETATM 7604 N1 ATP 800 -16.41 4 3.547 -7.525 1.00
> 43.25 N
> HETATM 7605 C2 ATP 800 -16.125 4.717 -8.076 1.00
> 43.37 C
> HETATM 7606 N3 ATP 800 -14.902 5.230 -8.032 1.00
> 43.76 N
> HETATM 7607 C4 ATP 800 -13.901 4.571 -7.417 1.00
> 44.09 C
> ________________________________________________
>
> and then changed the atoms name:
>
> ------------------------------------------------
> HETATM 7577 APG ATP 800 -4.997 4.425 -2.604& #160; 1.00
> 33.08 P
> HETATM 7578 OG1 ATP 800 -5.685 5.603 -1.764 1.00
> 33.76 O
> HETATM 7579 OG2 ATP 800 -3.427 4.765 -2.665 1.00
> 32.63 O
> HETATM 7580 OG3 ATP 800 -5.273 3.100 -1.967 1.00
> 33.16 O
> HETATM 7581 APB ATP 800 -5.173 3.787 -5.388 1.00
> 34.37 P
> HETATM 7582 OB1 ATP 800 -3.985 4.3 18 -6.120 1.00
> 33.33 O
> HETATM 7583 OB2 ATP 800 -5.232 2.335 -5.045 1.00
> 33.33 O
> HETATM 7584 OB3 ATP 800 -5.529 4.675 -4.089 1.00
> 33.22 O
> HETATM 7585 APA ATP 800 -7.773 3.348 -6.436 1.00
> 35.04 P
> HETATM 7586 OA1 ATP 800 -8.260 2.720 -5.177 1.00
> 33.60 O
> HETATM 7587 OA2 ATP 800 -7.501 2.503 -7.632 1.00
> 32.64 O
> HETATM 7588 OA3 ATP 800 -6.483 4.274 -6.168 1.00
> 34.07 O
> HETATM 7589 A5O ATP 800 -8.787 4.518 -6.833 1.00
> 36.40 O
> HETATM 7590 A5C ATP 800 -8.403 5.464 -7.846 1.00
> 39.10 C
> HETATM 7591 A4C ATP 800 -9.604 6.315 -8.269 1.00
> 41.61 C
> HETATM 7592 A4O ATP 800 60; -10.793 5.471 -8.462 1.00
> 42.22 O
> HETATM 7593 A3C ATP 800 -9.937 7.303 -7.152 1.00
> 41.81 C
> HETATM 7594 A3O ATP 800 -10.228 8.559 -7.756 1.00
> 43.61 O
> HETATM 7595 A2C ATP 800 -11.191 6.724 -6.514 1.00
> 42.05 C
> HETATM 7596 A2O ATP 800 -12.023 7.764 -6.036 1.00
> 41.49 O
> HETATM 7597 A1C ATP 800 -11.875 6.025 -7.679 1.00
> 42.90 C
> HETATM 7598 AN9 ATP 800 -12.608 4.832 -7.218 1.00
> 43.53 N
> HETATM 7599 AC8 ATP 800 -12.077 3.810 -6.547 1.00
> 43.35 C
> HETATM 7600 AN7 ATP 800 -13.023 2.904 -6.309 1.00
> 44.02 N
> HETATM 7601 AC5 ATP 800 -14.162 3.341 -6.835 1.00
> 44.22 C
> HETATM 7602 AC6 ATP 800 -15.461 160; 2.828 -6.899 1.00
> 44.02 C
> HETATM 7603 AN6 ATP 800 -15.751 1.647 -6.351 1.00
> 43.35 N
> HETATM 7604 AN1 ATP 800 -16.414 3.547 -7.525 1.00
> 43.25 N
> HETATM 7605 AC2 ATP 800 -16.125 4.717 -8.076 1.00
> 43.37 C
> HETATM 7606 AN3 ATP 800 -14.902 5.230 -8.032 1.00
> 43.76 N
> HETATM 7607 AC4 ATP 800 -13.901 ; 4.571 -7.417 1.00
> 44.09 C
> --------------------------------------------------
>
> Then i use the pdb2gmx, editconf, gromapp, (because I do EM in vacuum, so
> donnot use the genbox to add water).
> The .mdp file is:
> ---------------------------------------------------
> title = Minimization
> cpp = /lib/cpp
> include = -I../top
>
> integrator = steep
> emtol = 1.0
> nsteps = 200
> nstenergy = 10
> nstx tcout = 10
> xtc_grps = ATP
> energygrps = ATP
> nstlist = 1
> ns_type = simple
> rlist = 1.0
> coulombtype = cut-off
> rcoulomb = 1.0
> rvdw = 1.0
> constraints = none
> pbc = no
> -----------------------------------------
>
> Would you try this ATP use your .mdp file? Thank you!
>
> Best wishes!
>
> Duan
>
> ----------
>
>> Hi you need to explain in detail what steps you are doing before the
>> minimisation and also what parameters you are using in your .mdp file
>> because i have just run a minimisation of ATP (in water) to test the
>> topology in the GROMOS96 ff and it works fine for me, so there must > be
>> a problem in one of your setup steps or your simulation > > parameters.
>
>> Tom
>
>
----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.
---------- End Forwarded Message ----------
----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.
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