@Justin, thank you Justin. I will give it a try then. @Miro, sure,
I will look into it, thank you. - Yogesh On Fri, 31 Jan 2020 20:24:36 +0530
Miro Astore wrote Would topotools in vmd not work
in this context? I haven't used it but readabout it recently a
Would topotools in vmd not work in this context? I haven't used it but read
about it recently and it would seem this is the use case. Of course you
also need parameters. Wondering.
Best, Miro
Le sam. 1 févr. 2020 à 00:55, Justin Lemkul a écrit :
>
>
> On 1/31/20 8:25 AM, atb files wrote:
> >
>
On 1/31/20 8:25 AM, atb files wrote:
The files are given on the following server:https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated systems using NAMD.
If the individual topologies are not available anywhere, just a PSF,
then you will have to
The files are given on the following
server:https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated
systems using NAMD. -Yogesh On Thu, 30 Jan 2020 19:45:16 +0530 Justin
Lemkul wrote On 1/28/20 3:35 AM, atb files wrote: >
> >
On 1/28/20 3:35 AM, atb files wrote:
@Justin: the lipid is not yet added to the charmm directory. Any script?
How did you produce the original PSF?
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
O
@Justin: the lipid is not yet added to the charmm directory. Any
script?@Michele: pdb2gmx only works for proteins.-YogeshSent using Zoho
Mail On Mon, 27 Jan 2020 19:34:34 +0530 Justin Lemkul
wrote On 1/27/20 4:51 AM, atb files wrote:> >>
On 1/27/20 4:51 AM, atb files wrote:
Hello users,I have .pdb, .psf and .crd file for one system. How to use them (convert to itp) in Gromacs? Thanks. YogesgSent using Zoho Mail
Prepare the system with CHARMM-GUI and it will give you all t
Hi,
have you tried gmx pdb2gmx -f ?
Michele
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of atb files
Sent: 27 January 2020 10:51
To: gromacs.org_gmx-users
Subject: [gmx-users] Charmm to Gromacs itps
Hello users,I
Hello users,I have .pdb, .psf and .crd file for one system. How to
use them (convert to itp) in Gromacs? Thanks. YogesgSent using Zoho Mail
--
Gromacs Users mailing list
* Please search the archive at
ht
On 12/4/14 1:59 PM, Rebeca García Fandiño wrote:
Dear Gromacs users,
I am trying to obtain the .itp files for an organic molecule for a MD
simulation in GROMACS using the CHARMM force field.
I am trying to use cgenff_charmm2gmx.py:
python cgenff_charmm2gmx.py MOL1 ligand.mol2 ligand.str char
Dear Gromacs users,
I am trying to obtain the .itp files for an organic molecule for a MD
simulation in GROMACS using the CHARMM force field.
I am trying to use cgenff_charmm2gmx.py:
python cgenff_charmm2gmx.py MOL1 ligand.mol2 ligand.str charmm36-nov2014.ff
After this step, I obtain several fi
Dear Rebeca,
For small organic molecules you should use the portal
www.paramchem.org to do the initial atom typing. Then you can use the
python script found on the website of dr MacKerell
(http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs) to convert
the resulting str file to a Gromacs-frien
On 12/1/14 10:49 AM, Rebeca García Fandiño wrote:
Dear users,
I am trying to generate .itp files for simulating a small molecule in GROMACS
using the CHARMM force field.
Starting from a pdb, and using MATCH
MATCH.pl -forcefield top_all36_cgenff test.pdb
I obtain 3 files: test.rtf, top_test.r
Dear users,
I am trying to generate .itp files for simulating a small molecule in GROMACS
using the CHARMM force field.
Starting from a pdb, and using MATCH
MATCH.pl -forcefield top_all36_cgenff test.pdb
I obtain 3 files: test.rtf, top_test.rtf and test.prm
>From these files, I would like to o
Thank you Justin for the great help you have done, as you always been. I
will download the latest updated CHARMM36 files.
On Fri, Nov 7, 2014 at 6:10 PM, Justin Lemkul wrote:
>
>
> On 11/7/14 12:30 AM, Venkat Reddy wrote:
>
>> Dear Justin,
>> Please check the atom section of "toppar_all36_lipid_
On 11/7/14 12:30 AM, Venkat Reddy wrote:
Dear Justin,
Please check the atom section of "toppar_all36_lipid_cholesterol.str" file
that I pasted below.
* Toppar stream file for cholesterol. Stream following reading of
* top_all36_lipid.rtf and par_all36_lipid.rtf
!reference
!Suits, F., Pitman
Dear Justin,
Please check the atom section of "toppar_all36_lipid_cholesterol.str" file
that I pasted below.
* Toppar stream file for cholesterol. Stream following reading of
* top_all36_lipid.rtf and par_all36_lipid.rtf
!reference
!Suits, F., Pitman, M., MacKerell, A.D., Jr., Feller, S.E. "Mol
On 11/6/14 8:38 AM, Venkat Reddy wrote:
Dear Justin,
Yes, the problem is with the blank line at the end of atomtypes.atp. Now
its working fine. I have added the missing dihedral types from other
sources.
Thanks, I will fix that.
I have compared the cholesterol CHARMM parameters that are co
Dear Justin,
Yes, the problem is with the blank line at the end of atomtypes.atp. Now
its working fine. I have added the missing dihedral types from other
sources.
I have compared the cholesterol CHARMM parameters that are converted to
gromacs format and original parameters from
"toppar_all36_lipi
On 11/6/14 12:45 AM, Venkat Reddy wrote:
Dear Justin,
Thanks for the update. But unfortunately I couldn't find the parameters for
cholesteryl oleate. So, I tried to convert again the parameters from CHARMM
to GROMACS using these updated files:
./cgenff_charmm2gmx.py CHL1 CE-1.mol2 top_chol_est
Dear Justin,
Thanks for the update. But unfortunately I couldn't find the parameters for
cholesteryl oleate. So, I tried to convert again the parameters from CHARMM
to GROMACS using these updated files:
./cgenff_charmm2gmx.py CHL1 CE-1.mol2 top_chol_ester.rtf
/usr/local/gromacs/share/gromacs/top/c
On 11/5/14 10:23 AM, Venkat Reddy wrote:
Dear Justin,
While processing the lipid file using grompp, there was an error:
ERROR 1 [file chl1.itp, line 938]:
No default Proper Dih. types
ERROR 2 [file chl1.itp, line 939]:
No default Proper Dih. types
ERROR 3 [file chl1.itp, line 940]:
Dear Justin,
While processing the lipid file using grompp, there was an error:
ERROR 1 [file chl1.itp, line 938]:
No default Proper Dih. types
ERROR 2 [file chl1.itp, line 939]:
No default Proper Dih. types
ERROR 3 [file chl1.itp, line 940]:
No default Proper Dih. types
ERROR 4 [file c
Thank you Justin for the tip. I have given .rtf file as input and the
script has generated me the desired output .itp file. The command I used is
as shown below.
./cgenff_charmm2gmx.py CHL1 CE-1.mol2 top_chol_ester.rtf
/usr/local/gromacs/share/gromacs/top/charmm36.ff
Thank you very much Justin f
On 11/5/14 7:33 AM, Venkat Reddy wrote:
Dear Justin,
My lipid is cholesteryl oleate (CO). Since there are CHARMM36 parameters
available for cholesterol and oleate chain in POPC, I have clubbed both
together to generate the topology for CO (rtf file). Now I want to convert
this rtf to itp file.
Dear Justin,
My lipid is cholesteryl oleate (CO). Since there are CHARMM36 parameters
available for cholesterol and oleate chain in POPC, I have clubbed both
together to generate the topology for CO (rtf file). Now I want to convert
this rtf to itp file. is there any shortcut to accomplish this tas
On 11/5/14 7:03 AM, Venkat Reddy wrote:
Thank you Joao for the quick reply. My system has single lipid molecule and
I have pre- calculated charge information for every atom in the lipid. I
have edited charges on individual atoms apart from atom types.
By the way, Previous studies have reported
On 11/5/14 5:28 AM, João Martins wrote:
The rtp file is used by pdb2gmx for creating GROMACS topology and
coordinate files. Changing it in the lipids.rtp will not do much other than
allow you to generate from a pdb the .gro and .top for that molecule.
Changing atom types is tricky and should be
Thank you Joao for the quick reply. My system has single lipid molecule and
I have pre- calculated charge information for every atom in the lipid. I
have edited charges on individual atoms apart from atom types.
By the way, Previous studies have reported a topology for same lipid but in
NAMD conven
The rtp file is used by pdb2gmx for creating GROMACS topology and
coordinate files. Changing it in the lipids.rtp will not do much other than
allow you to generate from a pdb the .gro and .top for that molecule.
Changing atom types is tricky and should be avoided in order to make sure
you're using
Dear all,
I have a new lipid molecule and I want to simulate it using charmm36
forcefield. I have generated .str file using *paramchem* server and then
using the following command, I got the itp file.
./cgenff_charmm2gmx.py COL COL.mol2 COL.str charmm36.ff
Is this a reasonable approach for genera
Thanks a lot Justin, you have been very helpful.
> Date: Sat, 9 Aug 2014 05:02:20 -0600
> From: jalem...@vt.edu
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Charmm to gromacs
>
>
>
> On 8/9/14, 4:35 AM, Abu Naser wrote:
> > Thank you Justin.
On 8/9/14, 4:35 AM, Abu Naser wrote:
Thank you Justin. This is very useful for me. I have a question regarding
(and by -1 since CHARMM specifies these values as negative, but Gromacs uses a
different >convention)
I have been wondering what is the Gromacs' convention. Is it just the
ion?
> Date: Sat, 9 Aug 2014 03:39:07 -0600
> From: jalem...@vt.edu
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Charmm to gromacs
>
>
>
> On 8/8/14, 9:18 PM, Abu Naser wrote:
> >
> >
> >
> > Thanks Justin for your response.
> >
&g
0.1 (to convert A->nm).
-Justin
Date: Fri, 8 Aug 2014 08:50:16 -0600
From: jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Charmm to gromacs
On 8/8/14, 3:11 AM, Abu Naser wrote:
Hi All,
I took the following from Mark's script to convert non-bonded param
be converted.
> Date: Fri, 8 Aug 2014 08:50:16 -0600
> From: jalem...@vt.edu
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Charmm to gromacs
>
>
>
> On 8/8/14, 3:11 AM, Abu Naser wrote:
> > Hi All,
> >
> > I took the following from Mark
On 8/8/14, 3:11 AM, Abu Naser wrote:
Hi All,
I took the following from Mark's script to convert non-bonded parameters of ZN
manually:
printf("% 5s %f 0.0 A %.4g %.4g\n", $atom, $element_mass, 2*$four_epsilon
* $sigma**6, $four_epsilon * $sigma**12);
I am getting:
-0.0002245 -1.205e
Hi All,
I took the following from Mark's script to convert non-bonded parameters of ZN
manually:
printf("% 5s %f 0.0 A %.4g %.4g\n", $atom, $element_mass, 2*$four_epsilon
* $sigma**6, $four_epsilon * $sigma**12);
I am getting:
-0.0002245 -1.205e-08
instead of:
0.194215920555 1.046
On 7/9/14, 10:11 AM, Nikolaos Michelarakis wrote:
Hey,
Thanks a lot, I fixed the file but I am now getting a python error, I think.
Traceback (most recent call last):
File "./cgenff_charmm2gmx.py", line 792, in
m.read_mol2_coor_only(mol2_name)
File "./cgenff_charmm2gmx.py", line 7
Hey,
Thanks a lot, I fixed the file but I am now getting a python error, I think.
Traceback (most recent call last):
File "./cgenff_charmm2gmx.py", line 792, in
m.read_mol2_coor_only(mol2_name)
File "./cgenff_charmm2gmx.py", line 720, in read_mol2_coor_only
atomi = int(entry[0])-1
Va
On 7/9/14, 8:11 AM, Nikolaos Michelarakis wrote:
Hello again,
This what I have been trying to do so far. This is the command to run the
script:
./cgenff_charmm2gmx.py PTC 2e7z-ptc.mol2 2e7z-ptc.str charmm36-mar2014.ff
and this is the error I have been getting along with 2 Notes:
NOTE2: Plea
Hello again,
This what I have been trying to do so far. This is the command to run the
script:
./cgenff_charmm2gmx.py PTC 2e7z-ptc.mol2 2e7z-ptc.str charmm36-mar2014.ff
and this is the error I have been getting along with 2 Notes:
NOTE2: Please be sure to use the same version of CGenFF in your
On 7/2/14, 10:55 AM, Nikolaos Michelarakis wrote:
Dear Justin,
Thank you very much for your reply. I have tried the converter but I think
I don't have enough experience to get the CHARMM files working properly
with the converter. If I sent you the files, would it be possible to do it
for me or
Dear Justin,
Thank you very much for your reply. I have tried the converter but I think
I don't have enough experience to get the CHARMM files working properly
with the converter. If I sent you the files, would it be possible to do it
for me or guide me through it?
Thanks again,
Nicholas
On 23
On 6/23/14, 9:48 AM, Nikolaos Michelarakis wrote:
Dear All,
First, I would like to say that I have started using GROMACS during this
last month so please take that in mind when answering.
I am trying to run an MD simulation of an enzyme which contains some non
standard residues such as a tung
Dear All,
First, I would like to say that I have started using GROMACS during this
last month so please take that in mind when answering.
I am trying to run an MD simulation of an enzyme which contains some non
standard residues such as a tungsten metal ion and some other cofactors. I
understand
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