Yanmei Song wrote:
Dear Mark:
This error is being provoked at the top of the .rtp file when a line with
something like "[header]" is not parsing suitably. A while ago I suggested
using diff on the .rtp file. Do that.
Would you mind telling me how to do that in detail?
On a command line, "dif
Dear Mark:
This error is being provoked at the top of the .rtp file when a line with
something like "[header]" is not parsing suitably. A while ago I suggested
using diff on the .rtp file. Do that.
Would you mind telling me how to do that in detail?
I tried the following and it doesn't work.
d
Justin A. Lemkul wrote:
Then it seems clear to me that your installation of Gromacs is faulty.
Have you tried running the test set (available on the wiki site)? If
you can describe your computer system (OS, version, compilers used,
configuration options, etc.) then perhaps someone on the li
lem begins to
resemble
a nail.
-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song
Sent: Thursday, 30 April 2009 9:07 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
T
e a building block, you will need to do several
>>> things:
>>>
>>> 1. Re-number your .pdb file so that multiple monomers are apparent.
>>> 2. Use the + and - characters to indicate connectivity to the next
>>> residue
>>> and previous r
t a single PDM should contain only three atoms. Since what
>>> you
>>> are trying to do is make a building block, you will need to do several
>>> things:
>>>
>>> 1. Re-number your .pdb file so that multiple monomers are apparent.
>>> 2. Use the + and - cha
--
When the only tool you own is a hammer, every problem begins to resemble
a nail.
-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song
Sent: Thursday, 30 April 2009 9:07 AM
To: jalem...@vt.edu; Discussion list f
ou edit the file with?
>>>
>>> Catch ya,
>>>
>>> Dr. Dallas Warren
>>> Department of Pharmaceutical Biology and Pharmacology
>>> Pharmacy and Pharmaceutical Sciences, Monash University
>>> 381 Royal Parade, Parkville VIC 3010
>>
the file with?
>>>
>>> Catch ya,
>>>
>>> Dr. Dallas Warren
>>> Department of Pharmaceutical Biology and Pharmacology
>>> Pharmacy and Pharmaceutical Sciences, Monash University
>>> 381 Royal Parade, Parkville VIC 3010
&
ly tool you own is a hammer, every problem begins to resemble a nail.
-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song
Sent: Thursday, 30 April 2009 9:07 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re:
t;
>> -Original Message-
>> From: gmx-users-boun...@gromacs.org
>> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song
>> Sent: Thursday, 30 April 2009 9:07 AM
>> To: jalem...@vt.edu; Discussion list for GROMACS users
>> Subject: Re: [gmx-u
s.org] On Behalf Of Yanmei Song
> Sent: Thursday, 30 April 2009 9:07 AM
> To: jalem...@vt.edu; Discussion list for GROMACS users
> Subject: Re: [gmx-users] Error by pdb2gmx
>
> This is the new entry I added to the rtp file.
>
> [ PDM ]
>
>
> [ atoms ]
> SI
This is the new entry I added to the rtp file.
[ PDM ]
[ atoms ]
SI SI 0.300 1
CH3opls_0690.000 1
O opls_108 -0.300 1
[ bonds ]
SI O 0.190158805.0
SI CH3 0.164293160.0
[ dihedrals ]
CH3SIO
Yanmei Song wrote:
Dear Justin and Dallas:
Thank you for your help earlier.
I made a copy of ffoplsaa.rtp to my working directory and add a new
residue to it. Then perform the following command:
pdb2gmx -f pdms10.pdb -o pdms10.gro -p top.top -i pdms10.itp
Opening library file /packages/groma
Yanmei Song wrote:
---
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
Fatal error:
in .rtp file at line:
---
Well that's not a terribly helpful error message, is i
-users-boun...@gromacs.org] On Behalf Of Yanmei Song
>> Sent: Wednesday, 29 April 2009 9:24 AM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] Error by pdb2gmx
>>
>> Dear Dallas:
>>
>> Thanks for your response. It consists of many repe
gromacs.org
> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song
> Sent: Wednesday, 29 April 2009 9:24 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Error by pdb2gmx
>
> Dear Dallas:
>
> Thanks for your response. It consists of many r
Sent: Wednesday, 29 April 2009 8:59 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
Dear Justin:
Do you have any suggestions on how I can get the itp and gro file for
a very long polymer molecules (for example 500 united-atoms), which
only
-Original Message-
>> From: gmx-users-boun...@gromacs.org
>> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song
>> Sent: Wednesday, 29 April 2009 8:59 AM
>> To: jalem...@vt.edu; Discussion list for GROMACS users
>> Subject: Re: [gmx-users] Error by pdb2gmx
t: Wednesday, 29 April 2009 8:59 AM
> To: jalem...@vt.edu; Discussion list for GROMACS users
> Subject: Re: [gmx-users] Error by pdb2gmx
>
> Dear Justin:
>
> Do you have any suggestions on how I can get the itp and gro file for
> a very long polymer molecules (for exampl
Dear Justin:
Do you have any suggestions on how I can get the itp and gro file for
a very long polymer molecules (for example 500 united-atoms), which
only consists of Si, O and C atom. I can use PRODRG to generate a
short chain. But PRODRG has limitation of atom numbers in a molecule,
probably le
Yanmei Song wrote:
Dear All users:
I was trying to set up a long chain polymer system. I got the
following PDB file from WebLab. How can I make changes to the file in
order to make it as a GROMACS input pdb file. Then I can use pdb2gmx
to get the gro, itp and top file.
When I perform the pdb2
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