[gmx-users] parameters problem

[Nidhi Katyal]

To test swiss param parameters, I have generated *.pdb and *.itp files from
it. In the genbox command, I have used -ci *.pdb -nmol 2.
I have included *.itp in the topology as:

; Include Position restraint file
;#ifdef POSRES
;#include "posre.itp"
;#endif

;Include ligand topology
#include "ligand.itp"

; Include water topology
#include "charmm27.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "charmm27.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
LIG                 2
SOL             12904

But after I run grompp command, I get following error:

Fatal error:
Syntax error - File ligand.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes

Please help me rectify the problem of the order getting violated although
same worked for topology generated by PRODRG.

Thanks in advance.



On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/10/14, 8:21 AM, Nidhi Katyal wrote:
>
>> Thanks Justin. I would also like to know the reliability of parameters
>> generated using swiss param.
>>
>>
>>
> I have no personal experience with it.  My rule is to never trust anything
> from a black-box server without verifying it and assessing any information
> about penalties, deviations, etc. that it provides.
>
> -Justin
>
>
>  On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 3/10/14, 2:45 AM, Nidhi Katyal wrote:
>>>
>>>  Thank you Mark and Justin.
>>>> Now, I have carried out simulations using PME electrostatics and using
>>>> all other
>>>> parameters (except gromos 96 43a1 ff used) as suggested in
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>>>> gmx-tutorials/lysozyme/
>>>>
>>>> The protein is not loosing its structure now. But the problem is if I
>>>> carry out
>>>> simulations in the presence of experimentally known stabiliser generated
>>>> using
>>>> ProDrg (keeping all the parameters same while simulating both in the
>>>> presence
>>>> and absence of stabiliser), the partial loss of secondary structure is
>>>> observed
>>>> in the presence of stabilizer relative to the case in its absence at
>>>> 350K
>>>> thereby implying simulations going against experimental observations
>>>> (although
>>>> slight stabilization was observed at 300K). Simulations were repeated
>>>> twice with
>>>> two different force fields.
>>>> However if I use above em,pr,full parameters with cut-off
>>>> electrostatics,
>>>> although secondary structure is lost in the initial stages but I could
>>>> clearly
>>>> see the stabilization behaviour of additive in terms of secondary
>>>> structure
>>>> retainment till longer time. Is this observation a matter of chance-
>>>> reliable or
>>>> not? What could be the possible reason for not observing such
>>>> stabilization with
>>>> better parameters?
>>>>
>>>>
>>>>  Cutoff electrostatics are horribly inaccurate.  The fact that you
>>> conveniently see what you hope to when using a plain cutoff is likely by
>>> chance.
>>>
>>> The bigger issue is the use of PRODRG parameters.  As I have said
>>> numerous
>>> times on this list, the parameters it produces are demonstrably
>>> inaccurate
>>> and require reparametrization.
>>>
>>> http://pubs.acs.org/doi/abs/10.1021/ci100335w
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>> --
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>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
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