Sorry if I made someone more confuse, I thought this was the problem.
Probably reading the original post again would have a wise step.
Itamar
On Wed, Nov 11, 2009 at 7:25 PM, Tsjerk Wassenaar wrote:
> Hi,
>
> Well, -ignh is not the right answer here. I recall that just a few
> days ago someone p
Hi,
Well, -ignh is not the right answer here. I recall that just a few
days ago someone posted the same problem. For Amber you need to tag
the first and last residue. For your GLY, it means you have to rename
it to NGLY.
Itamar,
The warning mentions an atom missing from the .pdb file. These have
Hi,
Try to use -ignh.
On Wed, Nov 11, 2009 at 7:09 PM, leila karami wrote:
> I do command pdb2gmx but follow warning and error is came up:
>
> WARNING: atom H is missing in residue GLY 1 in the pdb file
> You might need to add atom H to the hydrogen database of residue
> GLY
>
I do command pdb2gmx but follow warning and error is came up:
WARNING: atom H is missing in residue GLY 1 in the pdb file
You might need to add atom H to the hydrogen database of residue
GLY
in the file ff???.hdb (see the manual)
Fatal error:
There were 1 missing atoms in molecu
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