[gmx-users] dna-drug simulations

[Justin Lemkul]

On 1/29/13 9:17 AM, amna khan wrote:
> hi,
> i want to simulate the DNA with gormacs forcefield, accrding to literatre
>   Charm and amber are best to be used but
> GROMACS96 43A1 force field can be also used
>
> the error with GROMACS96 43A1 is
> *Fatal error:*
> *Residue 'DA' not found in residue topology database*
>
> this is  same error with gromacs 43a2. gromacs 45 3a, gromacs 53a5, gromacs
> 53 a6 and opls/a
> [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
>   [DEPRECATED] Gromacs force field (see manual)   [DEPRECATED] Gromacs force
> field with hydrogens for N
>
>
>
> with charm force field is
> *Fatal error:*
> *Atom H7 in residue DA 1 was not found in rtp entry DA with 30 atoms*
> *while sorting atoms.*
> *
> *
> i have also use -ignh option, but stiill the problem comes which is as
> follows
> *Fatal error:*
> *Atom ''H5 in residue DA 1 was not found in rtp entry DA with 30 atoms*
> *while sorting ato*ms.
>
>
> for amber
> *Fatal error:*
> *Atom H7 in residue DA 1 was not found in rtp entry DA5 with 30 atoms*
> *while sorting atoms.*
>
>
> *and by -ignh command *
> *
> *
> *
> Fatal error:
> Atom ''H5 in residue DA 1 was not found in rtp entry DA5 with 30 atoms
> while sorting atoms.
>

The -ignh option will probably not work if the atom name is preceded by an 
apostrophe (') as you have here.  It appears your input .pdb file has some 
nonstandard naming.  If the atom was named H5, it would be ignored, but 'H5 is 
not detected as being a hydrogen.

>
> the error with charm and amber forcefiled are same
>
> *
> how to reomve this error for groamcs 43a1 or amber or chrm forcefield
>

Residues are named differently in each force field.  For instance, in the Gromos 
force fields, the names are DADE, DGUA, etc.  Thus the coordinate file must 
match the expectations of the force field (which is true for all force fields). 
  AMBER and CHARMM should work out of the box, and are far better options for 
doing nucleic acid simulations than Gromos.

-Justin

>
>
> On Sat, Jan 26, 2013 at 6:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/26/13 4:18 AM, amna khan wrote:
>>
>>> hi, all ,
>>>
>>> i want to simulate dna with ligand/drug
>>>
>>> i am getting error in generating he topology for dna .
>>>
>>
>> We can't help you unless you show us what the error is and provide (at the
>> very least) your exact pdb2gmx command.
>>
>>
>>   I'm unable to do using the  pdb2gmx with any of the force fields. Could
>>> anyone please tell if I can get any tutorial for the DNA-drug simulation.
>>>
>>
>> Exercise Google here.  If it exists, you should be able to find it by
>> searching or visiting gromacs.org.
>>
>>
>>   or which forcefield should i use ?
>>>
>>>
>> What does your analysis of the literature suggest would be the best choice?
>>
>> -Justin
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================