VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Jul 21 2017 - 17:00:38 CDT

Yup. Cutting cholesterol isn't something that was considered in model
development. Also, since it has those rings, cutting them would be
unwieldy. You may find that cholesterol partitions more readily to the
organic solvent than you might otherwise expect, as it gets squeezed out
of the lipids.
-Josh

On 07/21/2017 03:57 PM, Arthur Vale wrote:
> Dear Joshua Vermaas,
>
> The psf/pdb pair follow attached. By CLOL I meant cholesterol. I managed to go over the issue by changing the selection used by hmmmize so that it does not select the cholesterol atoms for cutting and it seems to work fine. I compared it to DCLE-HMMM systems generated by CHARMM-GUI and it also seems to not cut the cholesterol atoms, so I hope this is how the HMMM model is supposed to be used. Please, let me know if this assumption is correct.
>
> Best,
>
> Arthur Vale
> ________________________________________
> From: Vermaas, Joshua [Joshua.Vermaas_at_nrel.gov]
> Sent: Friday, July 21, 2017 4:07 PM
> To: Arthur Vale
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Building HMMM using patch files
>
> Hi Arthur,
>
> With respect to the autogenerate statements, it is fine to ignore the
> patch part, so long as you know what the patch statement means (see
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.charmm.org%2Fcharmm%2Fdocumentation%2Fby-version%2Fc41b1%2Fparams%2Fdoc%2Fstruct%2F%23Autogen&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C17ffeb867929425f313f08d4d0837466%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636362710520465916&sdata=%2FT9BARSIsF6jXO5HPXZ7mFdFSdr6%2FTnDcqc%2Fer6Pz3M%3D&reserved=0).
> The long and the short of it is that it tells CHARMM to regenerate
> angles and dihedrals after patches are applied. psfgen doesn't recognize
> this keyword.
>
> With respect to the CLOL problem, I don't actually know what CLOL should
> stand for (sorry!), so instead I can only guide you through the logic of
> the script. First, it looks for all atoms that have an atom name of C25
> or C35 (line 24), which in a normal lipid would be where you cut down
> the tails to make the short-tailed lipids. It then looks for atoms named
> C26 or C36 (line 33) bonded to C25 or C35 to start the cutting process.
> My guess is that CLOL had C25 or C35 atom names, but doesn't have the
> same tail naming nomenclature as the rest of CHARMM, so the patch didn't
> find the right atoms to connect together. You wouldn't happen to have a
> psf/pdb pair you could send over and let me play with?
>
> -Josh
>
> On 07/20/2017 08:32 PM, Arthur Vale wrote:
>> Dear Joshua Vermaas,
>>
>> I'm facing some problems with the HMMM. The first one of them is that when I source the charmm2hmmm.tcl script I get the following errors when psfgen tries to load the CHARMM topology files:
>>
>> For top_all36_lipid.rtf:
>> psfgen) ERROR! Failed to parse autogenerate statement. Line 74: AUTOGENERATE ANGLES DIHEDRALS PATCH
>>
>> For top_all36_cgenff.rtf:
>> psfgen) ERROR! Failed to parse autogenerate statement. Line 239: AUTO ANGLES DIHE PATCH
>>
>> Upon searching online I found a suggestion that changing those lines to:
>>
>> AUTOGENERATE ANGLES DIHEDRALS
>>
>> Would you happen to know if this is the appropriate way to solve this issue?
>>
>> In any case, if I do solve it this way, I notice that my CLOL molecules are not cut properly. Specifically, a CLOL H5R atom shows up fluctuating close to the new CLOL molecule. I didn't realize this issue until attempting to run my system with namd, at which point I get the error:
>>
>> FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG321 CTL3 (ATOMS 8773 8776)
>>
>> Both atoms belong to a single CLOL residue.
>>
>> After checking a DCLE-HMMM I previously generated with CHARMM-GUI I noticed that my cholesterols (which are name CHL1 instead of CLOL) seem to be unmodified. Therefore, I'm under the impression that the problem is that the charmm2hmmm.tcl patches the CLOL when it shouldn't. In any case, do you have any ideas on what might be happening?
>>
>> Thank you,
>>
>> Arthur Vale
>> ________________________________________
>> From: Vermaas, Joshua [Joshua.Vermaas_at_nrel.gov]
>> Sent: Thursday, July 20, 2017 4:35 PM
>> To: Arthur Vale; vmd-l_at_ks.uiuc.edu
>> Subject: Re: vmd-l: Building HMMM using patch files
>>
>> Hi Arthur,
>>
>> There was a goof during submission and publication, in that I forgot to include the script that goes along with the patch files and cuts the tails down for you. I've attached it here, as well as putting it on github for the folks that stumble into this thread at a later date (https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjvermaas%2Fhmmmsolvents&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C53dc6286df8348304de808d4cfe0c662%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636362011687962967&sdata=sBJwb09l9RLdADJel4SwanAab2j76aJzq3WE%2FkCi348%3D&reserved=0). Hopefully it is fairly self-explanatory, but basically you source the tcl script and use the "hmmmize" procedure.
>>
>> -Josh
>>
>> On 07/20/2017 03:23 PM, Arthur Vale wrote:
>> Dear All,
>>
>> Me and my group are attempting to turn a regular lipid membrane into an HMMM as described in this article: doi: 10.1021/acs.jpcb.6b11378. We have previously built HMMM membranes using CHARMM-GUI but we want to use the enhanced version of it described in the aforementioned paper. We have a pre-equilibrated regular lipid membrane generated through CHARMM-GUI lipid generator, as well as the files provided in the article. From reading the topology files we are under the impression that we can use the patches topology file to both cut the lipid tails and generate the SCSE solvent. Since previously we were successful doing the standard procedure with the autoPSF in VMD, we don't know how to actually proceed to apply these patches in order to achieve this. We tried doing it with the add patches in autoPSF as well as the patch command in psfgen but we were unsuccessful. Could anyone describe the steps to achieve this? I attached the contents of the topology and parameter files provided in the article below for re
ference.
>>
>> Thank you in advance,
>>
>> Arthur Vale
>>
>> ==> patches.top <==
>> !Patch to terminate C2 tail at carbon 5.
>> PRES C25T
>> ATOM C25 CTL3 -0.27
>> ATOM H5R HAL3 0.09
>> ATOM H5S HAL3 0.09
>> ATOM H5T HAL3 0.09
>> BOND C25 H5T
>>
>> !Patch to terminate C3 tail at carbon 5.
>> PRES C35T
>> ATOM C35 CTL3 -0.27
>> ATOM H5X HAL3 0.09
>> ATOM H5Y HAL3 0.09
>> ATOM H5Z HAL3 0.09
>> BOND C35 H5Z
>>
>> ==> top_scs.top <==
>> MASS 1 SCSM 14.027000 SC ! "Simple Carbon Solvent Methane"
>> MASS 2 SCSE 14.027000 SC ! "Simple Carbon Solvent Ethane"
>>
>> DEFA FIRS none LAST none
>> AUTOGENERATE ANGLES DIHEDRALS
>>
>> RESI SCSM 0.00
>> ATOM C SCSM 0.00
>>
>> RESI SCSE !Simple Carbon Solvent ethane
>> ATOM C1 SCSE 0.00
>> ATOM C2 SCSE 0.00
>> BOND C1 C2
>>
>> END
>>
>> ==> par_scs.prm <==
>> BONDS
>> SCSE SCSE 222.500 1.5300 ! CTL2-CTL2 bond parameter.
>>
>>
>> NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
>> cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
>> !adm jr., 5/08/91, suggested cutoff scheme
>> !
>> !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
>> !
>> !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
>> !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
>> !
>> !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
>> !
>>
>> SCSM 0.0 -0.350 2.080
>> SCSE 0.0 -0.112 2.080
>>
>> NBFIX
>> SCSM SCSM -0.625 3.15
>> SCSE SCSE -0.274 3.15
>>
>> END
>>
>>