Re: [gmx-users] Md simulation by Gromacs

[Erik Marklund]

Dear Maria,

Let’s keep this to the user list. I am first of all not a private tutor. 
Secondly, the answers you get (below) might be relevant for others.

> On 6 Apr 2017, at 16:04, maria khan  wrote:
> 
> Good evening Dear sir Erik Marklund..
> 
> I am very Thankful for your attention ..Actually i even dont know the basics 
> and one of the NAMD expert user told me so that gromacs use united atom ff 
> thats why gromacs is fast and NAMD use all atom thats why it is slow.
> 

That is incorrect. Gromacs can do both all-atom and united-atom. Gromacs can 
also make use of virtual sites, which allows for a longer time step, hence more 
simulated ns per hour. You can also choose not to. And then there are on top of 
that a number of reasons why gromacs is really fast without cutting (important) 
corners.

> Now my problems are : is there any option for considering hydrogen atom  to 
> process its calculation in MD run as last time when i did simulation i 
> applied the command of ignoring hydrogen atom ,,secondly what is the 
> difference Between ignoring h- atoms and considering it in MD running.I mean 
> would it effect the result of calculation after MD run..and if there is 
> option for taking h- atom as part of amino acid then why there is an option 
> for ignoring it..
> 

Please be specific. Are you referring to pdb2gmx -ignh? That just tells pdb2gmx 
to derive hydrogen positions and occupancies based on hydrogen bonding patterns 
and force-field-related information. It doesn’t normally produce topologies 
without hydrogens, and the hydrogens are thus part of the subsequent 
simulations. See the user-list archives. I know this has been discussed before. 
And you can also inspect the output files to see what they contain.

> Furthermore i dont know about forming parameters for my ligand thats is 
> alkaloid so im confuse how to form its parameter and if some one has 
> published its parameters then how i can find..i just need a stepwise protocol 
> for MD simulation,,most of the manuals are not understandable my majors are 
> pure biochemistry and mostly the explanations there are mathematica basedl.
> 

Well, parametrisation is not really for beginners. I also think others are more 
experienced in that area than I am.

> And yes i have studied the old version of manuals not updated one.
> 
> IF u have simplist form of manuals or any other stuff, kindly send me that i 
> very thankful. Last time u shared a paper of ur self but it was not my 
> research related.
> 

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Re: [gmx-users] md simulation by gromacs.

[Justin Lemkul]

On 10/28/16 2:50 PM, maria khan wrote:

Hello dear  gromacs users..
I am running simulation for protein ligand complex that are Glutamate
racemase and its inhibitor KRH.Bt it gives me error like" Atom HD1 in
residue HIS 61 was not found in rtp entry HISB with 12 atoms while sorting
atoms.For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt(it might
for instance have been H3, and we only expected H1 & H2).Note that
hydrogens might have been added to the entry for the N-terminus.Remove
this hydrogen or choose a different protonation state to solve it.Option
-ignh will ignore all hydrogens in the input."for making pdb2gmx and it
doesnt form topology file.
where am i doing wrong.
kindly help me out.


I answered this yesterday:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-October/109172.html

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] md simulation by gromacs.

[maria khan]

Hello dear  gromacs users..
I am running simulation for protein ligand complex that are Glutamate
racemase and its inhibitor KRH.Bt it gives me error like" Atom HD1 in
residue HIS 61 was not found in rtp entry HISB with 12 atoms while sorting
atoms.For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt(it might
for instance have been H3, and we only expected H1 & H2).Note that
hydrogens might have been added to the entry for the N-terminus.Remove
this hydrogen or choose a different protonation state to solve it.Option
-ignh will ignore all hydrogens in the input."for making pdb2gmx and it
doesnt form topology file.
where am i doing wrong.
kindly help me out.
Regards and thanks.
-- 
Gromacs Users mailing list

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