On 3/3/14, 8:13 PM, gromacs query wrote:
Hi Justin
Yes I chose termini 5TER or 3TER correctly but it only works fine when D*5
replaced by D* and D*3 by D* otherwise it ends with errors as said
previously.
As I would expect. Specific D*5/D*3 names are for AMBER force fields only.
-Justin
-
Hi Justin
Yes I chose termini 5TER or 3TER correctly but it only works fine when D*5
replaced by D* and D*3 by D* otherwise it ends with errors as said
previously.
thanks
JIom
On Tue, Mar 4, 2014 at 1:00 AM, Justin Lemkul wrote:
>
>
> On 3/3/14, 7:57 PM, gromacs query wrote:
>
>> Hi All
>>
>>
On 3/3/14, 7:57 PM, gromacs query wrote:
Hi All
Its in continuation. I am confused about something. In PDB file obtained
from NAB in AMBER I removed all Hydrogens and allow pdb2gmx to add them.
PDB has DC5 as starting and DT3 as end residue and I get this error:
pdb2gmx -ter -ff charmm36-jan2
Hi All
Its in continuation. I am confused about something. In PDB file obtained
from NAB in AMBER I removed all Hydrogens and allow pdb2gmx to add them.
PDB has DC5 as starting and DT3 as end residue and I get this error:
pdb2gmx -ter -ff charmm36-jan2014 -f test.pdb -o test.gro ( with or without
Hi Justin
Thanks it worked, just to add I have to use -ignh as well. I think it does
not detect some H at 5 end built from AMBER NAB programme.
Jiom
On Wed, Feb 5, 2014 at 3:13 PM, Justin Lemkul wrote:
>
>
> On 2/5/14, 9:49 AM, gromacs query wrote:
>
>> Hi All
>>
>> I have simple DNA pdb whi
On 2/5/14, 9:49 AM, gromacs query wrote:
Hi All
I have simple DNA pdb which has just 5 DA residues built from NAB in AMBER.
I am trying to use pdb2gmx with charmm36-jan2014.ff downloaded from:
http://mackerell.umaryland.edu/CHARMM_ff_params.html
pdb2gmx -f a.pdb -o gro.pdb -ff charmm36-ja
Hi All
I have simple DNA pdb which has just 5 DA residues built from NAB in AMBER.
I am trying to use pdb2gmx with charmm36-jan2014.ff downloaded from:
http://mackerell.umaryland.edu/CHARMM_ff_params.html
pdb2gmx -f a.pdb -o gro.pdb -ff charmm36-jan2014
I have changed all names according to
