Dear Justin,
The command line that got fatal error is:
gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh
-merge interactive
The command line that works fine is:
gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water spce -inter -ignh -merge
interactive
(just change
On 5/19/17 6:03 PM, Pandya, Akash wrote:
Tried to put it at the end but it still came up with the same error.
Justin, I don't understand what you mean?
If the file has been edited with a non-plain text editor then you can have
malformed return characters. Make sure you only ever edit file
On 5/19/17 6:31 PM, ZHANG Cheng wrote:
Dear Justin,
I replied the thread already, but it is waiting for approval due to large email
content. Could you please approve it?
I have no control over that. If it's too much for an email (normally pdb2gmx
output is fine) then upload to e.g. pasteb
Dear Justin,
I replied the thread already, but it is waiting for approval due to large email
content. Could you please approve it?
Cheng
---Original---
From: "ZHANG Cheng"<272699...@qq.com>
Date: 2017/5/19 22:37:52
To: "gromacs.org_gmx-users";
Cc: "QQ"<272699...@qq.com>;
Subject: pdb2gmx: At
Tried to put it at the end but it still came up with the same error.
Justin, I don't understand what you mean?
Akash
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: 1
On 5/19/17 5:37 PM, ZHANG Cheng wrote:
Dear Gromacs,
I got this fatal error after running "pdb2gmx":
Please provide your exact command and full screen output. There's a lot of
relevant information there, because pdb2gmx is doing a lot of complex things.
-Justin
Fatal error:
Residue 1
On 5/19/17 8:22 AM, Sailesh Bataju wrote:
Hi Sir,
You mean like choosing OPLS forcefield for all-atom model would be moer
appropriate for me?
At minimum, some all-atom force field, because whatever you were doing before
has no relationship to GROMOS and is unlikely to succeed.
Isobutane
Dear Gromacs,
I got this fatal error after running "pdb2gmx":
Fatal error:
Residue 1 named ASP of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fix
On 5/19/17 9:57 AM, Mohammad Hassan Khatami wrote:
First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf file
I found different linkages for beta-glucose, but non for alpha-glucose.
I am trying to make a simple chain with 1->4 linkages like below:
alpha-D-glucose,1->4,alph
On 5/19/17 5:33 PM, Mark Abraham wrote:
Hi,
Ok. Maybe it needs to be last in the molecules?
Or perhaps the error points to a malformed line ending that causes genion to
choke when updating the topology.
-Justin
Mark
On Fri, 19 May 2017 23:19 Pandya, Akash wrote:
It was the genion c
Hi,
Ok. Maybe it needs to be last in the molecules?
Mark
On Fri, 19 May 2017 23:19 Pandya, Akash wrote:
> It was the genion command. Here is the message.
>
> Fatal error:
> No line with moleculetype 'SOL' found the [ molecules ] section of file
> 'topol.top'
>
> -Original Message-
> Fr
It was the genion command. Here is the message.
Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
'topol.top'
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf
Hi,
Historically that was how things were done. Nobody thinks it is a good idea
any more. Use the Verlet scheme plus the recommendations for CHARMM
forcefields in GROMACS and you'll be fine - charge groups are removed
perforce.
Mark
On Fri, 19 May 2017 18:44 Dawid das wrote:
> Dear Gromacs Us
Hi,
I don't think grompp can issue that message. What was the message you
copied and pasted from your terminal?
Mark
On Fri, 19 May 2017 18:49 Pandya, Akash wrote:
> Hi all,
>
> I have received an error message shown below.
>
> Fatal error:
> No line with moleculetype 'SOL' found the [ molecul
Hi all,
I have received an error message shown below.
Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
'topol.top'
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
I don't under
Dear Gromacs Users,
I am a bit confused whether I shouldn't use charge
group-based cut-off for electrostatics when using CHARMM22.
If I shouldn't use it, what is the purpose of specification of charge
groups in
original CHARMM files?
Best wishes,
Dawid
--
Gromacs Users mailing list
* Please se
Hello,
I am running non-equilibrium simulations using the "acc-groups" command
and the Nose-Hoover thermostat. I just wanted to confirm that in Gromacs
code this additional acceleration is not considered to contribute to the
temperature when velocities are adjusted.
Thank you!
Jon
--
Gromacs
Hi Justin,
Thank you very much. It is Ok now.
Best,Mohammad
From: Justin Lemkul
To: Discussion list for GROMACS users
Sent: Tuesday, 16 May 2017, 18:34:14
Subject: Re: [gmx-users] Graphene modeling
On 5/16/17 7:31 AM, Mohammad Roostaie wrote:
> In addition, I used this comman
First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf file
I found different linkages for beta-glucose, but non for alpha-glucose.
I am trying to make a simple chain with 1->4 linkages like below:
alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.
Hi Sir,
You mean like choosing OPLS forcefield for all-atom model would be moer
appropriate for me?
Thank you.
On Fri, May 19, 2017 at 5:15 PM, Sailesh Bataju wrote:
> Hi Sir/Ma'am,
>
> I've finally created parameter file of isobutane using gromos54a7
> forcefield for all-atom model. Some of t
Dear users,
I have a 100 ns simulation trajectory and I have generated FEL (free energy
landscape) with it to extract a minimum energy conformation of my protein.
How can I show sampling convergence of FEL in gromacs? Do I have to split
the trajectory (say at every 20ns) and generate FELs from t
On 5/19/17 5:56 AM, abhisek Mondal wrote:
On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul wrote:
On 5/17/17 8:55 AM, abhisek Mondal wrote:
This time I think I got ligand restrained successfully during the umbrella
sampling. I have removed the restrain from protein, as per your advice.
Def
On 5/18/17 6:35 PM, Mohammad Hassan Khatami wrote:
Thanks Justin.
I have tried the CHARMM-GUI but it crashed. I might need to modify the order of
the atoms in my PDB file, which I have created using GLYCAM-Web GUI. I have
downloaded the “toppar_c36_feb16” but I did not find a manual on how to
On 5/19/17 7:30 AM, Sailesh Bataju wrote:
Hi Sir/Ma'am,
I've finally created parameter file of isobutane using gromos54a7
forcefield for all-atom model. Some of the parameters for bond angle
parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp
file in the relevant forcefie
Hi Sir/Ma'am,
I've finally created parameter file of isobutane using gromos54a7
forcefield for all-atom model. Some of the parameters for bond angle
parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp
file in the relevant forcefield, instead I used FTFE - CTFE - FTFE and
On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul wrote:
>
>
> On 5/17/17 8:55 AM, abhisek Mondal wrote:
>
>> This time I think I got ligand restrained successfully during the umbrella
>> sampling. I have removed the restrain from protein, as per your advice.
>> Defined the COM vector in md_umbrella
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