Hi,
Just add these entries in the NONBOND section of the frcmod
NONBON
FE 1.20000 0.05000 0.00000
LO 1.60000 0.20000 0.00000
LC 1.85 0.12 0.0
NP 1.8240 0.1700
NO 1.8240 0.1700
I hope it solves your problem now.
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Thakur, Abhishek [mailto:axt651.miami.edu]
Sent: Tuesday, April 18, 2017 9:40 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] HEME-CYS
Hi Dr.Martis,
Thank you so much.
I was working on it but now it ask me for vdW values
Building atom parameters.
For atom: .R<HEM 527>.A<FE 1> Could not find vdW (or other) parameters for type: FE For atom: .R<HEM 527>.A<NA 2> Could not find vdW (or other) parameters for type: NP For atom: .R<HEM 527>.A<NB 23> Could not find vdW (or other) parameters for type: NO For atom: .R<HEM 527>.A<NC 39> Could not find vdW (or other) parameters for type: NP For atom: .R<HEM 527>.A<ND 55> Could not find vdW (or other) parameters for type: NO
________________________________
From: Elvis Martis <elvis.martis.bcp.edu.in>
Sent: Tuesday, April 18, 2017 4:22:26 AM
To: AMBER Mailing List
Subject: Re: [AMBER] HEME-CYS
HI,
Have checked if all atoms names in the HEME match the frcmod file? I suspect that the frcmod file and prepin you have used are not compatible, I am maybe wrong though just a hunch.
When I loaded the heme_all.prepin and HEM.frcmod in leap with GAFF, I could reproduce your errors. However, this strange because the prepin and frcmod file don't look compatible hence my initial hunch.
Please try to load the attached frcmod and mol2 file I have attached. (You can ignore or replace entries in the frcmod file with comment line "added by Elvis" since they belong to the inhibitor I had used may not be useful for you.) Xleap Source leaprc.gaff Loadamberparams heme.frcmod HEM=loadmols HEM_CPD.mol2.
Once you have checked the atoms names in your HEM coordinates, make necessary changes.
Then you can load your protein only and try to make the FE-CYS bond.
Also, Have a closer look at this paper DOI: 10.1002/jcc.21922 Good luck.
Note: I have also attached the prmtop and inpcrd file for HEME only saved using the attached frmod and mol2 file.
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA W www.elvismartis.in<
http://www.elvismartis.in>
Skype. adrian_elvis12
-----Original Message-----
From: Thakur, Abhishek [mailto:axt651.miami.edu]
Sent: Tuesday, April 18, 2017 7:55 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] HEME-CYS
Hi Dr.Martis
I have tried by copying your values. Error which I am receiving is
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: S - FE Building angle parameters.
Could not find angle parameter: S - FE - NP Could not find angle parameter: S - FE - NO Could not find angle parameter: S - FE - NP Could not find angle parameter: S - FE - NO Could not find angle parameter: 2C - S - FE Building proper torsion parameters.
** No torsion terms for 2C-S-FE-NP
** No torsion terms for 2C-S-FE-NO
** No torsion terms for 2C-S-FE-NP
** No torsion terms for 2C-S-FE-NO
Building improper torsion parameters.
old PREP-specified impropers:
<HEM 527>: NA C1A C4A FE
<HEM 527>: NB C1B C4B FE
<HEM 527>: NC C1C C4C FE
<HEM 527>: ND C1D C4D FE
<HEM 527>: C1A C2A NA CHA
<HEM 527>: C1B C2B NB CHB
<HEM 527>: C1C C2C NC CHC
<HEM 527>: C1D C2D ND CHD
<HEM 527>: C2A C3A C1A CAA
<HEM 527>: C2B C3B C1B CMB
<HEM 527>: C2C C3C C1C CMC
<HEM 527>: C2D C3D C1D CMD
<HEM 527>: C3A C4A C2A CMA
<HEM 527>: C3B C4B C2B CAB
<HEM 527>: C3C C4C C2C CAC
<HEM 527>: C3D C4D C2D CAD
<HEM 527>: C4A NA C3A CHB
<HEM 527>: C4B NB C3B CHC
<HEM 527>: C4C NC C3C CHD
<HEM 527>: C4D ND C3D CHA
total 1580 improper torsions applied
20 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
I am attaching all the files for your reference.
When I have used the parameter file for HEM and CYS generated by
https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_tutorials_advanced_tutorial20_mcpbpy-5Fheme.htm&d=DwIFAw&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=09h5Lh_tbHMTl003W71eflOXdDsNPJPAZEKWriNVqpA&s=AiwYQAImapk5Od4ZHd4cCdtaof282Aw9aHwsWw4Dlng&e=
As our system is same I have got an error
Building topology.
Building atom parameters.
For atom: .R<HEM 527>.A<FE 1> Could not find vdW (or other) parameters for type: FE For atom: .R<HEM 527>.A<NA 2> Could not find vdW (or other) parameters for type: NP For atom: .R<HEM 527>.A<NB 23> Could not find vdW (or other) parameters for type: NO For atom: .R<HEM 527>.A<NC 39> Could not find vdW (or other) parameters for type: NP For atom: .R<HEM 527>.A<ND 55> Could not find vdW (or other) parameters for type: NO Parameter file was not saved.
REMARK GOES HERE, THIS FILE IS GENERATED BY MCPB.PY MASS
M1 55.85 Fe ion
Y1 32.06 2.900 S in cystine
Y2 14.01 0.530 Sp2 N in non-pure aromatic systems, identical to nc
Y3 14.01 0.530 Sp2 N in non-pure aromatic systems, identical to nc
Y4 14.01 0.530 Sp2 N in non-pure aromatic systems, identical to nc
Y5 14.01 0.530 Sp2 N in non-pure aromatic systems, identical to nc
BOND
Y1-M1 74.9 2.3197 Created by Seminario method using MCPB.py
Y2-M1 52.1 2.0761 Created by Seminario method using MCPB.py
Y3-M1 42.2 2.1137 Created by Seminario method using MCPB.py
Y4-M1 42.3 2.1133 Created by Seminario method using MCPB.py
Y5-M1 53.4 2.0723 Created by Seminario method using MCPB.py
CT-Y1 237.0 1.810 changed from 222.0 based on methanethiol nmodes
cc-Y2 525.4 1.3172 SOURCE3_SOURCE5 4612 0.0083
cc-Y3 525.4 1.3172 SOURCE3_SOURCE5 4612 0.0083
cc-Y4 525.4 1.3172 SOURCE3_SOURCE5 4612 0.0083
cc-Y5 525.4 1.3172 SOURCE3_SOURCE5 4612 0.0083
cd-Y2 441.1 1.3694 SOURCE1_SOURCE5 2269 0.0086
cd-Y3 441.1 1.3694 SOURCE1_SOURCE5 2269 0.0086
cd-Y4 441.1 1.3694 SOURCE1_SOURCE5 2269 0.0086
cd-Y5 441.1 1.3694 SOURCE1_SOURCE5 2269 0.0086
ANGL
CT-Y1-M1 62.03 106.09 Created by Seminario method using MCPB.py
Y1-M1-Y2 35.20 104.48 Created by Seminario method using MCPB.py
Y1-M1-Y3 36.64 100.33 Created by Seminario method using MCPB.py
Y1-M1-Y4 37.80 102.15 Created by Seminario method using MCPB.py
Y1-M1-Y5 33.52 106.70 Created by Seminario method using MCPB.py
Y2-M1-Y3 44.48 87.46 Created by Seminario method using MCPB.py
Y2-M1-Y4 43.43 153.31 Created by Seminario method using MCPB.py
Y2-M1-Y5 42.33 86.90 Created by Seminario method using MCPB.py
Y3-M1-Y4 46.27 86.03 Created by Seminario method using MCPB.py
Y3-M1-Y5 41.50 152.95 Created by Seminario method using MCPB.py
Y4-M1-Y5 43.71 87.24 Created by Seminario method using MCPB.py
cc-Y2-M1 64.80 127.11 Created by Seminario method using MCPB.py
cc-Y3-M1 81.21 124.83 Created by Seminario method using MCPB.py
cc-Y4-M1 67.10 126.47 Created by Seminario method using MCPB.py
cc-Y5-M1 77.47 126.28 Created by Seminario method using MCPB.py
cd-Y2-M1 80.38 125.81 Created by Seminario method using MCPB.py
cd-Y3-M1 65.56 127.28 Created by Seminario method using MCPB.py
cd-Y4-M1 78.87 125.05 Created by Seminario method using MCPB.py
cd-Y5-M1 66.90 127.26 Created by Seminario method using MCPB.py
CX-CT-Y1 50.0 108.60 AA cys (was CT-CT-SH)
Y1-CT-H1 50.0 109.50 AA cyx changed based on NMA nmodes
Y2-cc-cc 71.57 112.56 SOURCE3 141 4.2871
Y3-cc-cc 71.57 112.56 SOURCE3 141 4.2871
Y4-cc-cc 71.57 112.56 SOURCE3 141 4.2871
Y5-cc-cc 71.57 112.56 SOURCE3 141 4.2871
cc-Y2-cd 71.76 105.49 CORR_SOURCE5 1810 1.9032
cc-Y3-cd 71.76 105.49 CORR_SOURCE5 1810 1.9032
cc-Y4-cd 71.76 105.49 CORR_SOURCE5 1810 1.9032
cc-Y5-cd 71.76 105.49 CORR_SOURCE5 1810 1.9032
cd-cd-Y2 67.63 121.98 CORR_SOURCE5 141 1.9633
cd-cd-Y3 67.63 121.98 CORR_SOURCE5 141 1.9633
cd-cd-Y4 67.63 121.98 CORR_SOURCE5 141 1.9633
cd-cd-Y5 67.63 121.98 CORR_SOURCE5 141 1.9633
ce-cc-Y2 68.07 121.70 CORR_SOURCE5 58 1.4179
ce-cc-Y3 68.07 121.70 CORR_SOURCE5 58 1.4179
ce-cc-Y4 68.07 121.70 CORR_SOURCE5 58 1.4179
ce-cc-Y5 68.07 121.70 CORR_SOURCE5 58 1.4179
ce-cd-Y2 68.67 123.98 SOURCE4_SOURCE5 10 2.4097
ce-cd-Y3 68.67 123.98 SOURCE4_SOURCE5 10 2.4097
ce-cd-Y4 68.67 123.98 SOURCE4_SOURCE5 10 2.4097
ce-cd-Y5 68.67 123.98 SOURCE4_SOURCE5 10 2.4097
DIHE
X -cc-Y2-X 2 9.5 180.0 2.0 statistic value from parm94
X -cc-Y3-X 2 9.5 180.0 2.0 statistic value from parm94
X -cc-Y4-X 2 9.5 180.0 2.0 statistic value from parm94
X -cc-Y5-X 2 9.5 180.0 2.0 statistic value from parm94
X -cd-Y2-X 2 9.5 180.0 2.0 statistiv value from parm94
X -cd-Y3-X 2 9.5 180.0 2.0 statistiv value from parm94
X -cd-Y4-X 2 9.5 180.0 2.0 statistiv value from parm94
X -cd-Y5-X 2 9.5 180.0 2.0 statistiv value from parm94
CT-Y1-M1-Y2 3 0.00 0.00 3.0 Treat as zero by MCPB.py
CT-Y1-M1-Y3 3 0.00 0.00 3.0 Treat as zero by MCPB.py
CT-Y1-M1-Y4 3 0.00 0.00 3.0 Treat as zero by MCPB.py
CT-Y1-M1-Y5 3 0.00 0.00 3.0 Treat as zero by MCPB.py
CX-CT-Y1-M1 3 0.00 0.00 3.0 Treat as zero by MCPB.py
M1-Y1-CT-H1 3 0.00 0.00 3.0 Treat as zero by MCPB.py
M1-Y2-cc-cc 3 0.00 0.00 3.0 Treat as zero by MCPB.py
M1-Y3-cc-cc 3 0.00 0.00 3.0 Treat as zero by MCPB.py
M1-Y4-cc-cc 3 0.00 0.00 3.0 Treat as zero by MCPB.py
M1-Y5-cc-cc 3 0.00 0.00 3.0 Treat as zero by MCPB.py
Y1-M1-Y2-cc 3 0.00 0.00 3.0 Treat as zero by MCPB.py
Y1-M1-Y2-cd 3 0.00 0.00 3.0 Treat as zero by MCPB.py
Y1-M1-Y3-cc 3 0.00 0.00 3.0 Treat as zero by MCPB.py
Y1-M1-Y3-cd 3 0.00 0.00 3.0 Treat as zero by MCPB.py
Y1-M1-Y4-cc 3 0.00 0.00 3.0 Treat as zero by MCPB.py
Y1-M1-Y4-cd 3 0.00 0.00 3.0 Treat as zero by MCPB.py
Y1-M1-Y5-cc 3 0.00 0.00 3.0 Treat as zero by MCPB.py
Y1-M1-Y5-cd 3 0.00 0.00 3.0 Treat as zero by MCPB.py
Y3-cc-ce-cd 1 1.0 180.0 2.0 same as X -ce-ce-X
Y4-cc-ce-cd 1 1.0 180.0 2.0 same as X -ce-ce-X
Y5-cc-ce-cd 1 1.0 180.0 2.0 same as X -ce-ce-X
Y5-cd-ce-cc 1 1.0 180.0 2.0 same as X -ce-ce-X
cc-Y2-M1-Y3 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cc-Y2-M1-Y4 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cc-Y2-M1-Y5 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cc-Y3-M1-Y2 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cc-Y3-M1-Y4 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cc-Y3-M1-Y5 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cc-Y4-M1-Y2 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cc-Y4-M1-Y3 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cc-Y4-M1-Y5 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cc-Y5-M1-Y2 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cc-Y5-M1-Y3 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cc-Y5-M1-Y4 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cc-ce-cd-Y2 1 1.0 180.0 2.0 same as X -ce-ce-X
cc-ce-cd-Y3 1 1.0 180.0 2.0 same as X -ce-ce-X
cc-ce-cd-Y4 1 1.0 180.0 2.0 same as X -ce-ce-X
cd-Y2-M1-Y3 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-Y2-M1-Y4 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-Y2-M1-Y5 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-Y3-M1-Y2 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-Y3-M1-Y4 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-Y3-M1-Y5 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-Y4-M1-Y2 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-Y4-M1-Y3 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-Y4-M1-Y5 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-Y5-M1-Y2 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-Y5-M1-Y3 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-Y5-M1-Y4 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-cd-Y2-M1 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-cd-Y3-M1 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-cd-Y4-M1 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-cd-Y5-M1 3 0.00 0.00 3.0 Treat as zero by MCPB.py
cd-ce-cc-Y2 1 1.0 180.0 2.0 same as X -ce-ce-X
ce-cc-Y2-M1 3 0.00 0.00 3.0 Treat as zero by MCPB.py
ce-cc-Y3-M1 3 0.00 0.00 3.0 Treat as zero by MCPB.py
ce-cc-Y4-M1 3 0.00 0.00 3.0 Treat as zero by MCPB.py
ce-cc-Y5-M1 3 0.00 0.00 3.0 Treat as zero by MCPB.py
ce-cd-Y2-M1 3 0.00 0.00 3.0 Treat as zero by MCPB.py
ce-cd-Y3-M1 3 0.00 0.00 3.0 Treat as zero by MCPB.py
ce-cd-Y4-M1 3 0.00 0.00 3.0 Treat as zero by MCPB.py
ce-cd-Y5-M1 3 0.00 0.00 3.0 Treat as zero by MCPB.py
ha-ce-cc-Y2 1 1.0 180.0 2.0 same as X -ce-ce-X
ha-ce-cc-Y3 1 1.0 180.0 2.0 same as X -ce-ce-X
ha-ce-cc-Y4 1 1.0 180.0 2.0 same as X -ce-ce-X
ha-ce-cc-Y5 1 1.0 180.0 2.0 same as X -ce-ce-X
ha-ce-cd-Y2 1 1.0 180.0 2.0 same as X -ce-ce-X
ha-ce-cd-Y3 1 1.0 180.0 2.0 same as X -ce-ce-X
ha-ce-cd-Y4 1 1.0 180.0 2.0 same as X -ce-ce-X
ha-ce-cd-Y5 1 1.0 180.0 2.0 same as X -ce-ce-X
IMPR
Y3-cd-cd-ce 1.1 180.0 2.0 Using default value
Y4-cd-cd-ce 1.1 180.0 2.0 Using default value
Y2-cd-cd-ce 1.1 180.0 2.0 Using default value
Y4-cc-cc-ce 1.1 180.0 2.0 Using default value
Y5-cc-cc-ce 1.1 180.0 2.0 Using default value
Y2-cc-cc-ce 1.1 180.0 2.0 Using default value
Y5-cd-cd-ce 1.1 180.0 2.0 Using default value
Y3-cc-cc-ce 1.1 180.0 2.0 Using default value
NONB
M1 1.3860 0.0135709700 IOD set for Fe3+ ion in TIP3P water from Li et al. JPCB, 2015, 119, 883
Y1 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's
Y2 1.8240 0.1700 OPLS
Y3 1.8240 0.1700 OPLS
Y4 1.8240 0.1700 OPLS
Y5 1.8240 0.1700 OPLS
________________________________
From: Elvis Martis <elvis.martis.bcp.edu.in>
Sent: Monday, April 17, 2017 4:31:14 PM
To: AMBER Mailing List
Subject: Re: [AMBER] HEME-CYS
These parameters are partly from Cheatham et al and two entries I have made.
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA W www.elvismartis.in<
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.elvismartis.in&d=DwIFAw&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=09h5Lh_tbHMTl003W71eflOXdDsNPJPAZEKWriNVqpA&s=TxmVVsh2JSp264Ve8NuHNg53GG2gIIMabKB3FrE0V5Q&e= > Skype. adrian_elvis12
-----Original Message-----
From: Thakur, Abhishek [mailto:axt651.miami.edu]
Sent: Monday, April 17, 2017 11:27 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] HEME-CYS
Thank you so much Dr.Martis
I am using CYM.
Can you let me know from where you have got this parameter?
________________________________
From: Elvis Martis <elvis.martis.bcp.edu.in>
Sent: Monday, April 17, 2017 6:10:21 AM
To: AMBER Mailing List
Subject: Re: [AMBER] HEME-CYS
Hi,
It seems the frcmod you are using has no parameters for FE-S (CYS) or you did not change the residue name from CYS to CYM.
In the former case try adding the following to the corresponding sections in your frcmod file and in the latter case just change the res name to CYM.
BOND
fe-SH 39.00 2.565
ANGLE
SH-fe-nc 48.00 87.595 # average angle
SH-fe-nd 48.00 87.595 # average angle
CT-SH-fe 39.00 105.885
DIHEDRAL
CT-SH-fe-nc 1 0.00 180.000 2.000
CT-SH-fe-nd 1 0.00 180.000 2.000
SH-fe-nd-cd 1 0.00 180.000 2.000
SH-fe-nd-cc 1 0.00 180.000 2.000
cc-nc-fe-SH 1 0.000 180.000 2.000
cd-nd-fe-sh 1 0.000 180.000 2.000
Hope this helps.
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA W www.elvismartis.in<
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.elvismartis.in&d=DwIFAw&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=Zc_mFxqbyKTwxWio2j2Oq56QS1ummsFtS9la1SvWz0E&s=KS_nVJbep5R9_umFQpghrrmPEhbIhzOZ2LqJGLDmQNY&e=> Skype. adrian_elvis12
-----Original Message-----
From: Thakur, Abhishek [mailto:axt651.miami.edu]
Sent: Monday, April 17, 2017 10:16 PM
To: amber.ambermd.org
Subject: [AMBER] HEME-CYS
Hi
I am having a system in which HEME FE is bounded to Cys S.
When I am using HEME amber parameters and manually giving bond between FE and S, I am getting an error
Could not find bond parameter for: SH - FE Building angle parameters.
Could not find angle parameter: SH - FE - NP Could not find angle parameter: SH - FE - NO Could not find angle parameter: SH - FE - NP Could not find angle parameter: SH - FE - NO Could not find angle parameter: CT - SH - FE Building proper torsion parameters.
** No torsion terms for CT-SH-FE-NP
** No torsion terms for CT-SH-FE-NO
** No torsion terms for CT-SH-FE-NP
** No torsion terms for CT-SH-FE-NO
How should I solve this problem.
with regards,
-AT
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Received on Tue Apr 18 2017 - 22:00:02 PDT
