On 3/31/16 10:41 AM, Brett wrote:
Dear Justin and All,
The full screen output was as following and I am looking forward to getting a
reply from you.
gmx pdb2gmx -f practice.pdb -o target_processed.gro -ignh
:-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:
Dear Justin and All,
The full screen output was as following and I am looking forward to getting a
reply from you.
gmx pdb2gmx -f practice.pdb -o target_processed.gro -ignh
:-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:
GROMACS is written by:
On 3/31/16 8:18 AM, Brett wrote:
Dear Justin and All,
For terminal residue, regardless I select 0, 1, 2, the error messages always
exist.
I have opened the pdb by swiss deep view and resaved it, the same error message
still exist.
However if I choose force field 6: AMBER99SB-ILDN
Dear Justin and All,
For terminal residue, regardless I select 0, 1, 2, the error messages always
exist.
I have opened the pdb by swiss deep view and resaved it, the same error message
still exist.
However if I choose force field 6: AMBER99SB-ILDN protein, the error message
disappear.
Will
On 3/30/16 10:41 PM, Brett wrote:
Dear All,
When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro -ignh" with force
field, it gave me the warning as following,
"WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was
mapped
to an entry in the topology database,
Dear All,
When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro -ignh" with
force field, it gave me the warning as following,
"WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction
