On 7/2/14, 4:40 AM, Dawid das wrote:
I have managed to deal with this problem in following way:
In topology file some bonding parameters were actually missing but some
bonding parameters were not needed, e.g. U-B or dihedral parameters for
atoms which are not connected, that is they belong to
On 7/2/14, 9:22 AM, Dawid das wrote:
2014-07-02 13:50 GMT+02:00 Justin Lemkul jalem...@vt.edu:
The problems almost certainly stem from the manipulations you've made to
the angles and dihedrals. I don't understand why you've commented some of
them out. For instance, the first angle that
Beside that, why do you say that 978-992 are bonded? According to visual
inspection of mCherry7-solv-ion.gro there is no connection between them (as
it should be) and also in mCherry7.top there is no bonding parameter for
them.
2014-07-02 15:22 GMT+02:00 Dawid das add...@googlemail.com:
Excuse me but I don't think we understand each other. If there are three
atoms for instance and two of them are bonded and the third is not then how
can I obtain or derive parameters for them? That is what I do not
understand.
2014-07-02 15:29 GMT+02:00 Dawid das add...@googlemail.com:
Beside
On 7/2/14, 9:29 AM, Dawid das wrote:
Beside that, why do you say that 978-992 are bonded? According to visual
inspection of mCherry7-solv-ion.gro there is no connection between them (as
it should be) and also in mCherry7.top there is no bonding parameter for
them.
Inspection of a coordinate
O'right, I'ill do that but I have also noticed visually something strange.
The thing is that for my new residue there is no bond shown between two
atoms although the distance between them is correct and usual for C-S
single bond.
I used vmd and opened *.gro file. May that be a problem?
On 6/30/14, 5:12 AM, Dawid das wrote:
O'right, I'ill do that but I have also noticed visually something strange.
The thing is that for my new residue there is no bond shown between two
atoms although the distance between them is correct and usual for C-S
single bond.
I used vmd and opened
O'right, firstly I have tried to do all the calculations once again for my
complete protein system and I got the same error but also something more:
ERROR 1 [file mCherry7.top, line 18152]:
No default U-B types
ERROR 2 [file mCherry7.top, line 18153]:
No default U-B types
ERROR 3 [file
O'right, I have solved this last problem for a new system.
Here's a link to all the files:
http://www.speedyshare.com/EEXq4/ff-trouble.tar.gz
Thank you for your help!
2014-06-30 18:13 GMT+02:00 Dawid das add...@googlemail.com:
O'right, firstly I have tried to do all the calculations once
On 6/30/14, 2:23 PM, Dawid das wrote:
O'right, I have solved this last problem for a new system.
Here's a link to all the files:
http://www.speedyshare.com/EEXq4/ff-trouble.tar.gz
Thank you for your help!
2014-06-30 18:13 GMT+02:00 Dawid das add...@googlemail.com:
O'right, firstly I have
On 6/27/14, 2:02 AM, Dawid das wrote:
2014-06-27 1:54 GMT+02:00 Justin Lemkul jalem...@vt.edu:
If the force field you're using uses U-B angles, you should stick to that.
If you don't need the cross-term, just specify ub0 and kub as zero, while
leaving sensible values for theta0 and ktheta.
So with what diagnostic shall I provide you with?
2014-06-27 13:50 GMT+02:00 Justin Lemkul jalem...@vt.edu:
On 6/27/14, 2:02 AM, Dawid das wrote:
2014-06-27 1:54 GMT+02:00 Justin Lemkul jalem...@vt.edu:
If the force field you're using uses U-B angles, you should stick to
that.
If
Dear Gromacs experts,
I have succesfuly put new atom types into force field expression.
I have managed to run pdb2gms, editconf and genbox.
But when I try
grompp -f minimize.mdp -c mCherry7-solv.gro -p mCherry7.top -o minimize.tpr
then I get an error saying that one od my newly inctroduced atoms
On 6/26/14, 1:47 PM, Dawid das wrote:
Dear Gromacs experts,
I have succesfuly put new atom types into force field expression.
I have managed to run pdb2gms, editconf and genbox.
But when I try
grompp -f minimize.mdp -c mCherry7-solv.gro -p mCherry7.top -o minimize.tpr
then I get an error
Thank you so much, but I run into another trouble:
Generated 29890 of the 29890 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 26783 of the 29890 1-4 parameter combinations
---
Program grompp, VERSION 4.5.5
I have just checked with original ffbonded.itp and the onyl difference is
that I added new atomtypes.
2014-06-26 20:58 GMT+02:00 Dawid das add...@googlemail.com:
Thank you so much, but I run into another trouble:
Generated 29890 of the 29890 non-bonded parameter combinations
Generating 1-4
I have figured out that I don't really need those U-B parameters, so I
changed function type to 1, and deleted those two last columns of zeros.
But I still get exactly the same error.
2014-06-26 21:05 GMT+02:00 Dawid das add...@googlemail.com:
I have just checked with original ffbonded.itp and
On 6/26/14, 3:15 PM, Dawid das wrote:
I have figured out that I don't really need those U-B parameters, so I
changed function type to 1, and deleted those two last columns of zeros.
But I still get exactly the same error.
If the force field you're using uses U-B angles, you should stick to
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