[gmx-users] Re: \\[gmx\\-users\\] The energy minimization\\.\\.\\.\\.

[TJ Piggot]

As i say keep things to the list please.

With regards to the files no as you should be able to fix the problem on 
your own as this will help you more in the long run. Try redoing every step 
making sure you do it correctly (especially the editing of the .rtp file)

Tom

--On 18 August 2007 10:58 +0800 MoJie Duan <mjduan at smail.hust.edu.cn> wrote:

> Hi,tom:
> Thank you for you help!
> Could you provid me the run file about the EM of my ATP molecule? (the
> .gro, .top, and .gro&.top files after editconf, the .tpr after grompp...
> maybe also the ff******.trp and ff*****.hdb you used). I will check which
> step have problems.
>
> And if i solve this problem, i will introduce my experience of resolving
> this problem in gmx-user for the beginner.
>
> Best regards!
> Duan
>
>
> 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 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
> & gt; 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.
>
>



----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.