Quoting Blaise Mathias-Costa [EMAIL PROTECTED]:
hello all,How to get the topology for a ligand, for which there is no
information available with the gromacs default libraries!! Thanks in
advanceBlaise
Try PRODRG:
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/
-Justin
Hi Antonello,
Note that parameterization of compounds is not for the faint of heart
(http://wiki.gromacs.org/index.php/Parameterization). For chitosan,
you first want to get the parameters for one building block right. In
case you want to use the GROMOS force field, search papers of Roberto
Lins,
Dear gromacs users,
i apply to your kind attention to know if someone have already parametrized the
chitosan structure.
I am trying to do it but with poor results.
Can you help me?
Thanking in advance
Dipartimento di Medicina Sperimentale
Universita' degli Studi di Parma
Hi,
Please describe clearly your poor results.
Regards,
Yang Ye
On 7/31/2007 10:55 PM, Antonello wrote:
Dear gromacs users,
i apply to your kind attention to know if someone have already parametrized the
chitosan structure.
I am trying to do it but with poor results.
Can you help me?
Hi all! I'm just a beginner user of Gromacs, that's why my question may
seem strange to you. But I hope, that somebody can help me in solving my
problem. The point is that I'm trying to perform the analysis of
tetrabutylammonium cation solvatation using OPLS force field. Earlier i've
Hi Mitch, thanks.
I'd like to use the OPLSA ff, to compare with other simulations that
I've run. So I can use the PRODRG to build an initial, then look at the
OPLSA ff to modify it, as you've suggested. I was just wondering if
there was a quick and easy way to do it, but I guess not!
Arneh,
How does one build a topology using a different force field (say for
instance, oplsaa)? Is there a simple way to do it,
I think OpenEye (or someone else, I forget whom) has some sort of
automatic parameterization tool for OPLS that automatically generates
parameters. Of course,
On 2/17/2007 12:01 PM, Hu Zhongqiao wrote:
Arneh,
How does one build a topology using a different force field (say for
instance, oplsaa)? Is there a simple way to do it,
I think OpenEye (or someone else, I forget whom) has some sort of
automatic parameterization tool for OPLS
Mark Abraham wrote:
---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 1180
Fatal error:
Incorrect number of parameters - found 4, expected 6 or 12.
---
This is being
Title: creating topology files
Fellow gmx users,
I am trying to create a topology file for TFE using the olpsaa/l force field to simulate a peptide in a mixed solvent. I created a molecule.itp file (as it was suggested in the manual), a molecule.gro file for TFE and I was able to place
Owen, Michael wrote:
Fellow gmx users,
I am trying to create a topology file for TFE using the olpsaa/l force
field to simulate a peptide in a mixed solvent. I created a
molecule.itp file (as it was suggested in the manual), a molecule.gro
file for TFE and I was able to place the several
dear list,
to get a topology for norleucine i combined parameters from LEU (N,CA,CB, plus
H´s, C, O) and MET (CG, CE, plus H´s). to get CD and its H´s i took parameters
from MET CG as well. finally i adjusted the charges of CG and CD to get a
residue topology with zero charge. can it be that
merc mertens wrote:
dear list,
to get a topology for norleucine i combined parameters from LEU (N,CA,CB, plus
H´s, C, O) and MET (CG, CE, plus H´s). to get CD and its H´s i took parameters
from MET CG as well. finally i adjusted the charges of CG and CD to get a
residue topology with zero
Hello everyone,
I have been having trouble with a topology I created
for androst-5-ene-3,17-dione (GROMOS 96 force field).
I have found the molecule to bend inwards withing 100
ps of equilibration, something which has not been seen
by others who have used CHARMM or AMBER. I have also
tried to
Hello,
I have been having trouble with a topology I created
for androst-5-ene-3,17-dione (GROMOS 96 force field).
I have found the molecule to bend inwards withing 100
ps of equilibration, something which has not been seen
by others who have used CHARMM or AMBER. I have also
tried to convert the
Hi all,
Has anybody built a gromax topology for selenomethionine?
How the topology can be incorporated into the existing gromacs topology
files?
thanks in advance.
sridhar
--
Sridhar Acharya, M
Senior Research Fellow
Lab of Computational Biology
CDFD, Gandipet Campus
Hyderabad. AP. INDIA
Sridhar Acharya wrote:
Hi all,
Has anybody built a gromax topology for selenomethionine?
How the topology can be incorporated into the existing gromacs topology
files?
It might exist on the website. You just need to replace the sulphur by
Se, probably with a slightly larger sigma. Check
Title: No topology
I just want to generate the topology of one protein with water. Previously I had obtained the archive .gro from a .pdb, I used editconf to make a box after I used genbox to add waters to protein. The archive .gro is generated but I have tried many times and with other
Edgar Mixcoha Hernández wrote:
I just want to generate the topology of one protein with water.
Previously I had obtained the archive .gro from a .pdb, I used editconf
to make a box after I used genbox to add waters to protein. The archive
.gro is generated but I have tried many times and with
Anthony Cruz wrote:
Thank you for your answer. I find it to day searching the mailing list because
I have some problems with the mail and I dont receive this mail. I try the
beta version but I got confised because i dont see the GROMOS terminology ej.
gb_x, ga_x ect.
If I use the beta version
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