Re: [gmx-users] define a new residue

? Thaankks! :)   Sincerely, Shima From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, July 9, 2012 12:35 AM Subject: Re: [gmx-users] define a new residue On 7/8/12 12:43 PM, Shima Arasteh wrote: OK. What

[gmx-users] define a new residue

Hi dear gmx friends, I got the parameters of formyl-valine through the CHARMM website. Now I need to define it as a new residue FVAL( as Justin suggested me earlier) in .rtp file. To set the correct charges for atoms, I used the CHARMM output. In order to define FVAL to rtp file, I added these

Re: [gmx-users] define a new residue

for your suggestions. Cheers, Shima From: francesco oteri francesco.ot...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, July 8, 2012 3:04 PM Subject: Re: [gmx-users] define a new

Re: [gmx-users] define a new residue

list for GROMACS users gmx-users@gromacs.org Sent: Sunday, July 8, 2012 3:28 PM Subject: Re: [gmx-users] define a new residue Why have you removed the hydrogen?  2012/7/8 Shima Arasteh shima_arasteh2...@yahoo.com Dear Francesco, Thanks. Honestly I thought about this, but I don't know how much

Re: [gmx-users] define a new residue

, 2012 3:28 PM Subject: Re: [gmx-users] define a new residue Why have you removed the hydrogen? 2012/7/8 Shima Arasteh shima_arasteh2...@yahoo.com Dear Francesco, Thanks. Honestly I thought about this, but I don't know how much charges I need to increase or decrease of other atoms

Re: [gmx-users] define a new residue

...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Shima Arasteh shima_arasteh2...@yahoo.com Sent: Sunday, July 8, 2012 4:44 PM Subject: Re: [gmx-users] define a new residue Usually in CHARMM the sidechains are parametrized as separate blocks and than merged to the backbone

Re: [gmx-users] define a new residue

On 7/8/12 11:29 AM, Shima Arasteh wrote: Thanks all. So if I find a protein which is parametrized by CHARMM and then find the valine residue there, I might use the parameters of side chains of it in my own rtp file. Right? You can look this up in the force field's .rtp file. For full

Re: [gmx-users] define a new residue

for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, July 8, 2012 9:02 PM Subject: Re: [gmx-users] define a new residue On 7/8/12 11:29 AM, Shima Arasteh wrote: Thanks all. So if I find a protein which is parametrized by CHARMM and then find the valine residue there, I might use the parameters

Re: [gmx-users] define a new residue

On 7/8/12 12:43 PM, Shima Arasteh wrote: OK. What about generating an output file through CGenFF by the first 3 residues of the protein, rather thn the first 2 (formyl+valine)? Maybe. Try it and see, rather than waiting a few hours for someone to get around to replying :) -Justin --

Re: [gmx-users] define a new residue

;) Anyway, thanks!   Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, July 9, 2012 12:35 AM Subject: Re: [gmx-users] define a new residue On 7/8/12 12:43 PM, Shima Arasteh wrote

[gmx-users] Define a new residue in oplsaa

Dear GROMACS users, I wanna add add a FOR residue containing atom C and O. In oplsaa force field, the most similar residue to formyl (FOR) is ACE. How I can change the ACE in .rtp file in oplsaa ff to define FOR residue as a new residue? I did like this, Is it correct? [ ACE ]  [ atoms ]    CH3 

Re: [gmx-users] Define a new residue in oplsaa

Shima Arasteh wrote: Dear GROMACS users, I wanna add add a FOR residue containing atom C and O. In oplsaa force field, the most similar residue to formyl (FOR) is ACE. How I can change the ACE in .rtp file in oplsaa ff to define FOR residue as a new residue? I did like this, Is it correct?

Re: [gmx-users] Define a new residue in oplsaa

:* Justin A. Lemkul jalem...@vt.edu *To:* Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, April 14, 2012 9:19 PM *Subject:* Re: [gmx-users] Define a new residue in oplsaa Shima Arasteh wrote: Dear GROMACS users, I wanna add add

Re: [gmx-users] Define a new residue in oplsaa

Thank you so much. Shima From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, April 14, 2012 9:28 PM Subject: Re: [gmx-users] Define a new residue in oplsaa Shima Arasteh wrote: Dear Justin