Re: a topology file in VMD

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Wed Apr 25 2007 - 10:07:49 CDT

Just check for
RESI PCGL
PRES EST1
PRES EST2
inside
vmd/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp
I apologize for my mistake. RESI STEA comes within charmm 32b1.
c32b1/toppar/top_all27_prot_lipid.rtf

Regards
Cesar

SMAHANE CHALABI escribió:
> Hi Dear,
>
> I thank you for your response. But could you give me the exact name of
> the two different residues two different residues PCGL and STEA and
> patches EST1 EST2, because I use CHARMM22 I have access to the
> topology file of the lipids but I didn't find the residues, which you
> called PCGL, STEA, EST1 and EST2.
>
> Yours sincerely,
> Smahane.
>
>
>
>> From: Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar>
>> To: SMAHANE CHALABI <smahane_chalabi_at_hotmail.com>, namd-l_at_ks.uiuc.edu
>> Subject: Re: namd-l: a topology file in VMD
>> Date: Wed, 25 Apr 2007 10:58:01 -0300
>>
>> Hi there,
>> Since you are going to use charmm topology and parameter files I
>> suggest first reading the documentation on
>>
>> http://www.charmm.org/document/Charmm/c32b2/rtop.html
>> http://www.charmm.org/document/Charmm/c32b2/parmfile.html
>>
>> DSPC can be built joining two different residues PCGL and STEA and
>> patches EST1 EST2.
>> I think there are no parameters for arachidoyl tails so you will have
>> to develop them.
>>
>> Topology and parameter files provided with vmd can be found at
>> vmd/plugins/noarch/tcl/readcharmmpar1.0/par_all27_prot_lipid_na.inp
>> vmd/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp
>>
>> Regards
>> Cesar
>>
>>
>>
>> SMAHANE CHALABI escribió:
>>>
>>> Dear all,
>>>
>>> I have to generate a phospholipid monolayer composed by
>>> distearoylphosphatidylcholine (DSPC) and
>>> diarachidoylphosphatidylcholine (DAPC). But these phospholipids are
>>> not known in VMD version 1.8.6, which is able to generate a
>>> phospholipid bilayer composed by POPE or POPC as we can see in the
>>> text consol window such as:
>>>
>>> Usage: membrane -l <lipid> -x <xsize> -y <ysize> {-o <prefix>}
>>> <lipid> is lipid name (POPC or POPE; others as added)
>>> <xsize> and <ysize> are membrane sizes in X and Y (Angstroms)
>>> <prefix> is optional output file prefix (default "membrane").
>>>
>>> However, I don’t know how to construct the template box structures
>>> for DAPC and DSPC. I have seen that there is a combined CHARMM
>>> All-Hydrogen topology file for proteins and lipids, which contains
>>> POPC and POPE topologies. So, I will certainly have to create a
>>> topology file for DSPC and DAPC, but I don't know the format of this
>>> topology file and its exactly localization.
>>>
>>> Moreover, is there any way in VMD to construct a phospholipid
>>> monolayer only and not a bilayer?
>>>
>>> Thanks.
>>>
>>> Yours sincerely,
>>> Smahane CHALABI
>>>
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>>
>
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