It would be helpful if all of this was on one thread, with replies
embedded. I have sent several replies to your questions, all of which
have gone unacknowledged. It makes it very difficult for anyone (myself
or someone else) to give advice if we don't know what you're doing or
what you've
Dear Justin,
I am absolutely sorry for the discomfort. Since this is the first time I am
using Gromacs, so things are not clear to me so I am trying things very
randomly thats why I could not keep update the things. Here I restarted
every thing and have a look at and let me know your suggestions:
Hi!
I'm new to Gromacs, so maybe my answer is not 100% correct, but it seems
to me that you forgot to create the required insu_pwi2MM.gro file. In
your last pdb2gmx command you just created insu_pwi2MM.pdb, and then the
last grompp command cannot found the insu_pwi2MM.gro file. I think you
rams rams wrote:
Dear Justin,
I am absolutely sorry for the discomfort. Since this is the first time
I am using Gromacs, so things are not clear to me so I am trying
things very randomly thats why I could not keep update the things.
Here I restarted every thing and have a look at and let
Hi,
I mistyped the command as you mentioned. I did used the following:
grompp -f eminimization.mdp -c insu_pwi2MM.pdb -p insu_pwi.top -o
MM_insu.tpr
Now the error is the following:
turning all bonds into constraints...
NOTE:
System has non-zero total charge: -2.00e+00
processing
is that fine if i change the SOL number in the top file created at the first
step ?
On Mon, Jun 30, 2008 at 1:50 PM, rams rams [EMAIL PROTECTED] wrote:
Here's where your problem is. This step is unnecessary! Once you have the
topology, there is no need to re-process with pdb2gmx. Once you
HI,
When I use the merge command along with pdb2gmx to form inter disulphide
bonds between two different chains, its removing a water molecule to connect
the two ends. Its like forming a peptide bond which I dont wish. Is there
any way to tell to gromacs, to create the inter dishulphide bonds
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