[gmx-users] Micelle Modeling

2011-07-12 Thread Janowicz, Adrianna C.
Users, I'm trying to start a micelle modeling project & have tried countless approaches to making a DPC micelle. My problems include: -DPC not being recognized when I try to imput it into the [molecules] seciton of the topology file to account for the DPC molecules in the water topology. Otherwise,

Re: [gmx-users] Micelle Modeling

2011-07-12 Thread Janowicz, Adrianna C.
Also, I forgot to mention that I need to throw a protein into the mix. How would I get both the protein and the DPC into the box? On Tue, July 12, 2011 10:46 am, Justin A. Lemkul wrote: > > > Janowicz, Adrianna C. wrote: >> Users, >> I'm trying to start a micelle mod

Re: [gmx-users] Micelle Modeling

2011-07-25 Thread Janowicz, Adrianna C.
tin A. Lemkul wrote: > > > Janowicz, Adrianna C. wrote: >> Also, I forgot to mention that I need to throw a protein into the mix. >> How >> would I get both the protein and the DPC into the box? >> >> > > Have a look through some of the more advanced tutorials

Re: [gmx-users] Micelle Modeling

2011-07-26 Thread Janowicz, Adrianna C.
ARNING 1 [file dpc.top, line 28]: >> 18915 non-matching atom names >> atom names from dpc.top will be used <=(taken from 1 dpc.itp x 65) >> atom names from dpc.gro will be ignore <=(made from 65 dpc molecule pdb) On Mon, July 25, 2011 8:21 am, Justin A. Lemkul wro

Re: [gmx-users] Micelle Modeling

2011-07-26 Thread Janowicz, Adrianna C.
0 ; qtot: 0 On Tue, July 26, 2011 1:16 pm, Justin A. Lemkul wrote: > > > Janowicz, Adrianna C. wrote: >> Im sorry for the confusion. >> I used an .itp file from the UCalgary site for dpc, I input a line >> >> [ molecules ] >> ; mole

[gmx-users] (no subject)

2011-08-08 Thread Janowicz, Adrianna C.
I'm trying to install gromacs-3.3 & am constantly getting errors regarding configure: error: C++ preprocessor "/lib/cpp" fails sanity check or CC non executable. Is this because my version of Linux is too new because these errors were not happening when I installed the newest versions of Gromacs?

[gmx-users] Re:

2011-08-22 Thread Janowicz, Adrianna C.
Janowicz, Adrianna C. wrote: I'm trying to install gromacs-3.3 & am constantly getting errors regarding configure: error: C++ preprocessor "/lib/cpp" fails sanity check or CC non executable. Is this because my version of Linux is too new because these errors were not happeni

[gmx-users] UNK not found in residue topology

2011-11-11 Thread Janowicz, Adrianna C.
Hello, I'm getting an UNK not found in residue topology error message. I figured out what the error was and tried to add carbon to ffopslaa.rtf but it was unsucessful. What can I do/How can I change my pdb file from UNK so that Carbon and Hydrogen can be recognized? (I built my own hydrocarbon st

[gmx-users] UNK not found in residue topology

2011-11-14 Thread Janowicz, Adrianna C.
Hello, I'm getting an UNK not found in residue topology error message. After I run pdb2gmx -f XXX.pdb -o conf.pdb Fatal error: Residue 'UNK' not found in residue topology database I figured out what the error was and tried to add UNK as carbon to ffopslaa.rtf [UNK] [ atoms ] UNK

[gmx-users] UNK not found

2011-11-21 Thread Janowicz, Adrianna C.
The following is a part of a .pdb file I generated. HETATM 250 C1 UNK 1 18.454 11.417 22.519 1.00 0.00 C HETATM 251 C2 UNK 1 19.297 10.247 22.595 1.00 0.00 C HETATM 252 C3 UNK 1 19.949 9.511 21.410 1.00 0.00 C HETATM