On 10/31/18 10:56 AM, Raji wrote:
Thank you for your valuable inputs. Yes i did checked ether
parameters, diethylether have O-C (alkyl) bonding parameter as CC32A
OC30A CC32A. but i dont find a parameter related to C(aromatic)-O
bonding. similar one is tyrosine CA-OH1, but it may need
Thank you for your valuable inputs. Yes i did checked ether
parameters, diethylether have O-C (alkyl) bonding parameter as CC32A
OC30A CC32A. but i dont find a parameter related to C(aromatic)-O
bonding. similar one is tyrosine CA-OH1, but it may need validation on
torsion terms?? can you please
On 10/30/18 12:12 PM, Raji wrote:
Hi
Thank you for your input.
1. when attaching the alkyl chain with OH group in the aminoacid, to
represent the bonded term C(aromatic)-O-C (alkyl). i took O as OC301 and
C(alkyl) as CT2. But there is no bonded term for CA-OC301. How to import
this by
21:13:34 -0400
> From: Justin Lemkul
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Adding residue to .rtp file
> Message-ID:
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 10/24/18 2:46 PM, Raji wrote:
> > Thank you for your reply.
On 10/24/18 2:46 PM, Raji wrote:
Thank you for your reply. I have few more questions
1. Yes, command pdb2gmx continued and generated the topology. The warning
is about 74 atoms which are from the new added rtp entry. I just want to
understand more about the warning. I dont find any related
t; From: Justin Lemkul
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Adding residue to .rtp file
> Message-ID:
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 10/18/18 11:45 AM, Raji wrote:
> > Hi,
> >
> > I have added the modifi
On 10/18/18 11:45 AM, Raji wrote:
Hi,
I have added the modified residue entry in the rtp file and able to
generate to topology and .gro file. but i got this warning when passing the
pdb2gmx command.What is this about?
"WARNING: there were 74 atoms with zero occupancy and 0 atoms with
Hi,
I have added the modified residue entry in the rtp file and able to
generate to topology and .gro file. but i got this warning when passing the
pdb2gmx command.What is this about?
"WARNING: there were 74 atoms with zero occupancy and 0 atoms with
occupancy unequal to one (out of 160
On 10/5/18 10:23 AM, Raji wrote:
Thank you for your reply.
"stitching an alkyl group to an existing amino acid should be very
straightforward without having to parametrize the entire molecule"
Can you please explain me how to do that?
Functional groups can generally be used like building
Thank you for your reply.
"stitching an alkyl group to an existing amino acid should be very
straightforward without having to parametrize the entire molecule"
Can you please explain me how to do that?
Thanks
Raji
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Subject: Re: [gmx-users] Adding residue to .rtp file
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On 10/4/18 11:28 AM, Raji wrote:
Thank you for your reply. I am trying to simulate this peptide in gromacs
with CHARMM36
On 10/4/18 11:28 AM, Raji wrote:
Thank you for your reply. I am trying to simulate this peptide in gromacs
with CHARMM36 force field. Thatswhy i converted the parameters from CGenFF
to CHARMM format. So How to proceed further. I assume i cant treat it like
The first step is to not use
Thank you for your reply. I am trying to simulate this peptide in gromacs
with CHARMM36 force field. Thatswhy i converted the parameters from CGenFF
to CHARMM format. So How to proceed further. I assume i cant treat it like
as a protein ligand complex, because there is covalent bond between TYR
On 10/3/18 5:15 PM, Raji wrote:
Hi
I would like to simulate a peptide, in which alkyl chain is covalently
linked with aminoacid. I have generated the topology for alkyl chain with
CGenFF and converted to CHARMM format. Now how to include this parameters
in the aminoacid rtp file. If the
Hi
I would like to simulate a peptide, in which alkyl chain is covalently
linked with aminoacid. I have generated the topology for alkyl chain with
CGenFF and converted to CHARMM format. Now how to include this parameters
in the aminoacid rtp file. If the alkyl chain is bonded with aminoacid
On 4/26/16 2:57 AM, Md. Imrul Reza Shishir wrote:
Dear All
I have a structure file(pdb) cellulose fibril with unknown residue and
atom type. I want to add this residue in the .rtp file and .hdb file. As i
am new in gromacs. Is there any tutorial how i parameterize the structure
file with
Dear All
I have a structure file(pdb) cellulose fibril with unknown residue and
atom type. I want to add this residue in the .rtp file and .hdb file. As i
am new in gromacs. Is there any tutorial how i parameterize the structure
file with force field. Is there any tutorial or guideline how to
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