Hi,
Okay, they're read in some cases. But not in pdb2gmx related to
building a topology as far as I can see. I should've written:
pdb2gmx doesn't distinguish between ATOM and HETATM entries.
pdb2gmx does not read CONECT records.
Now the 'TER' recoord... That makes a difference.
Cheers,
Tsjerk
Tsjerk Wassenaar skrev:
Hi Jack,
On Thu, Jan 14, 2010 at 5:41 PM, Jack Shultz
mailto:j...@drugdiscoveryathome.com>> wrote:
Problem Solved.
I replaced HETATM with ATOM, I fixed BOTH N-terminal and
C-terminal. I kept TER and END. Removed all CONECT. Renamed the
CYS to CYS
Hi Jack,
On Thu, Jan 14, 2010 at 5:41 PM, Jack Shultz
wrote:
> Problem Solved.
>
> I replaced HETATM with ATOM, I fixed BOTH N-terminal and C-terminal. I kept
> TER and END. Removed all CONECT. Renamed the CYS to CYS2. No other
> non-AminoAcid residues were present. Most of this is described by
Problem Solved.
I replaced HETATM with ATOM, I fixed BOTH N-terminal and C-terminal. I kept
TER and END. Removed all CONECT. Renamed the CYS to CYS2. No other
non-AminoAcid residues were present. Most of this is described by the
FFAmber site
http://chemistry.csulb.edu/ffamber/
2)
*(!) Residue N
Jack Shultz wrote:
Well some of the problems in the log relate to unresolved exceptions
processing the ligands, those ligands are skipped. But I should probably
just test the receptors seperate from the workflow and merged ligands. I
will check this list provided by Tsjerk. Possibly the numbe
Well some of the problems in the log relate to unresolved exceptions
processing the ligands, those ligands are skipped. But I should probably
just test the receptors seperate from the workflow and merged ligands. I
will check this list provided by Tsjerk. Possibly the numbering is off.
Anyway its t
Hi Jack, Justin,
Is this related to last weeks post? I suggested that you might have
seen long bond warnings, which in this case certainly show up. Lots of
them. But one stands out: there's a break in the chain of 3.3 nm!
During minimization an attempt is made to bring these ends together,
which c
On 1/10/10 9:47 PM, Jack Shultz wrote:
Thanks Justin,
I went back to the original pdb files. These were conformations of the
same protein derived from molecular dynamics simulations performed by
Andrey.
What I intially attempted was preping the structures using tleap, hoping
to paint in missing
Thanks Justin,
I went back to the original pdb files. These were conformations of the same
protein derived from molecular dynamics simulations performed by Andrey.
What I intially attempted was preping the structures using tleap, hoping to
paint in missing atoms for residues. Then use this to rep
On 1/10/10 5:18 PM, Jack Shultz wrote:
I am trying to get this workflow opperational. However, my systems are
getting unstable. I have preped two mdp files: 1) one for restrained 2)
unrestrained. LINCS errors appear for restrained and unrestrained has
infinite energy appearing.
http://boinc.dru
I am trying to get this workflow opperational. However, my systems are
getting unstable. I have preped two mdp files: 1) one for restrained 2)
unrestrained. LINCS errors appear for restrained and unrestrained has
infinite energy appearing.
http://boinc.drugdiscoveryathome.com/*em_restrained_rcs_md
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