Re: [gmx-users] Adding missing heavy atoms

2015-07-26 Thread Justin Lemkul
On 7/22/15 1:00 PM, prasun kumar wrote: Dear Justin and tarak Thanx alot for the reply If I have base atoms, so I have stacking information also. I was curious to know whether by changing the forcefield information will help me or not. For example, when I need ADNA, I will use some other info

Re: [gmx-users] Adding missing heavy atoms

2015-07-22 Thread prasun kumar
Dear Justin and tarak Thanx alot for the reply If I have base atoms, so I have stacking information also. I was curious to know whether by changing the forcefield information will help me or not. For example, when I need ADNA, I will use some other information related to it and like that it conti

Re: [gmx-users] Adding missing heavy atoms

2015-07-11 Thread Justin Lemkul
On 7/11/15 1:03 AM, prasun kumar wrote: Dear All I have generated the base atoms of nucleotides in a structure, but it does not have sugar and phosphate atoms. Is there any method by which I can add them appropriately (either in A or B form) If you already have the base configuration, you ca

Re: [gmx-users] Adding missing heavy atoms

2015-07-10 Thread tarak karmakar
Hi Prasun, If you really want to prepare the structure of a molecule, better try any modelling software. GaussView could be a handy option. Export your molecule in .pdb format and a little bit of modification will make your nucleotide ready to use. Best wishes, Tarak On Sat, Jul 11, 2015 at 10:33

[gmx-users] Adding missing heavy atoms

2015-07-10 Thread prasun kumar
Dear All I have generated the base atoms of nucleotides in a structure, but it does not have sugar and phosphate atoms. Is there any method by which I can add them appropriately (either in A or B form) Thanx in advance PRASUN (ASHOKA) Desire + stability = Resolution Resolution + Hard work = Succes