Dear tianchuan1015,
Yes, It seems the heme_all.frcmod is successfully load into leap.
Dont worry, ignore these errors and proceed for next steps.
For heme you dont need to do any changes in protein and heme.
these files are working fine (I already tried these files for your complex
here)
Only thing is to re-prepare ligand parameters (frcmod) file.
So, No need to modify anything in your protein and heme.
These are parameters for heme with Cys bound state. (same is the case in
your CYP).
All the best
On Fri, Feb 22, 2013 at 8:01 PM, tianchuan1015 <tianchuan1015.gmail.com>wrote:
> **
> Dear Prajwal Nandekar <prajwal.pharm07.gmail.com>,
> I really appreciate for your help! I used the files you offered. But
> when I load heme_all.frcmod, there comes errors as follows:
>
> > loadamberparams heme_all.frcmod
> Loading parameters: ./heme_all.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> Force field modifications for all-atom heme
> Unknown keyword:
> in parameter file.
> Unknown keyword: NP in parameter file.
> Unknown keyword:
> in parameter file.
> Unknown keyword: CX in parameter file.
> Unknown keyword:
> in parameter file.
>
> Besides, the heme forms disulfide linkage with residue cys. I
> have changed CYS to CYX. Is this enough or what else should I modify.
>
> sincerely,
> tianchuan
> ------------------------------
> tianchuan1015
>
> *From:* Prajwal Nandekar <prajwal.pharm07.gmail.com>
> *Date:* 2013-02-22 18:12
> *To:* tianchuan1015 <tianchuan1015.gmail.com>; AMBER Mailing List<amber.ambermd.org>
> *Subject:* Re: [AMBER] amber error about protein containing heme
> Dear tianchuan56,
>
> I think you are CYP450 system with heme and ligand.
> The problem is in the "frcmod.hemeall" and "heme_all.in" files. These
> files doesn't have proper parameters for heme.
> I have validated prepin and frcmod files of heme [attached in mail
> filename (1) heme_all.prepin and (2) heme_all.frcmod].
> Please use those files for system preparation.
>
> commands in tleap or xleap:
> loadamberprep heme_all.prepin
> loadamberparams heme_all.frcmod
>
> One more thing I observed in frcmod file of ligand (R.frcmod) is also not
> properly defined bond angle and atom types.
> Please re-prepare it.
>
> In your CYP-ligand complex, The distance between some atoms of ligand R is
> in close proximity to some atoms of heme. (I.e. these are in bonding
> distance) This condition should not be happen in case of CYP450s.
> Please pay attention towards these issues.
>
> All the best
>
>
> On Fri, Feb 22, 2013 at 1:28 PM, tianchuan1015 <tianchuan1015.gmail.com>wrote:
>
>> Dear amber specialists,
>> When I am simulating the interaction betweem drug and protein containing
>> heme, the parameter of heme was not identified.
>> Amber has generated the drug.lib and drug.frcmod, heme_all.in and
>> frcmod.hemall are downloaded. All the four files have been loaded in tleap
>> successfully. But the protein complex could not be saved
>> as follows:
>> > saveamberparm RRR complex-solvated.prmtop complex-solvated.inpcrd
>> Checking Unit.
>> WARNING: There is a bond of 4.977567 angstroms between:
>> ------- .R<R 494>.A<C11 19> and .R<R 494>.A<C13 21>
>> WARNING: There is a bond of 5.471636 angstroms between:
>> ------- .R<R 494>.A<C4 12> and .R<R 494>.A<C6 14>
>> WARNING: There is a bond of 3.329748 angstroms between:
>> ------- .R<R 494>.A<N 5> and .R<R 494>.A<C3 11>
>> WARNING: There is a bond of 7.987354 angstroms between:
>> ------- .R<R 494>.A<S 1> and .R<R 494>.A<C 8>
>> FATAL: Atom .R<HEM 493>.A<CHA 1> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CHB 2> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CHC 3> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CHD 4> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C1A 5> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C2A 6> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C3A 7> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C4A 8> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CMA 9> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CAA 10> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CBA 11> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CGA 12> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<O1A 13> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<O2A 14> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C1B 15> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C2B 16> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C3B 17> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C4B 18> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CMB 19> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CAB 20> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CBB 21> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C1C 22> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C2C 23> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C3C 24> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C4C 25> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CMC 26> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CAC 27> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CBC 28> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C1D 29> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C2D 30> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C3D 31> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<C4D 32> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CMD 33> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CAD 34> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CBD 35> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<CGD 36> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<O1D 37> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<O2D 38> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<NA 39> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<NB 40> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<NC 41> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<ND 42> does not have a type.
>> FATAL: Atom .R<HEM 493>.A<FE 43> does not have a type.
>> My parameter files are also attached.
>>
>>
>>
>> tianchuan56
>>
>>
>>
>>
>> tianchuan1015
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> --
> *Thanks and Regards,
>
> ---------------------------------------------
> Prajwal Nandekar
> Ph. D. Scholar
> Department of Pharmacoinformatics
> National Institute of Pharmaceutical Education and Research (NIPER)
> Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
> Mob. 09780741228*
>
--
*Thanks and Regards,
---------------------------------------------
Prajwal Nandekar
Ph. D. Scholar
Department of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research (NIPER)
Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
Mob. 09780741228*
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Received on Fri Feb 22 2013 - 09:00:03 PST
