AMBER Archive (2009)

Subject: Re: [AMBER] too many undefined parameters in frcmod

From: Jason Swails (jason.swails_at_gmail.com)
Date: Thu Oct 22 2009 - 06:59:55 CDT

Pang,
Francois's suggestion should certainly work. However, it looks like you're
filling in ff99/ff94 parameters using gaff, so it's naming all of the atoms
for ff99/ff94 (upper-case letters), but it's pulling the parameters from
gaff.dat (lower-case letters). Another thing you can do is use the '-a'
flag when you actually run parmchk. This will cause parmchk to print out
ALL parameters to the frcmod file that you'e creating.

Good luck!
Jason

On Thu, Oct 22, 2009 at 5:37 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:

> Dear Pang xueqin,
>
> You could follow two different approaches for your organic structure:
>
> 1) You use parm99 FF atom types (with capital letters): you need to load
> the "parm99.dat" file in LEaP to load all the required FF parameters.
>
> source leaprc.ff99SB
> MOL = loadmol2 YOUR-MOL.mol2
> saveamberparm MOL MOL.top MOL.crd
>
> => LEaP will not save the prmtop/prmcrd files - if missing FF parameters
> are found, but LEaP will list the missing force field parameters.
> For instance, you have the CA-HA FF parameters describing the CA-HA bond in
> your frcmod file: This "CA-HA" FF parameters should be in parm99.dat; you
> should not need to add them in your frcmod file.
>
> Then, you create a frcmod file with these missing FF parameters (if LEaP
> detects missing FF parameters) that you load in a second step:
>
> source leaprc.ff99SB
> FRCMOD = loadamberparams your-frcmod-file
> MOL = loadmol2 YOUR-MOL.mol2
> saveamberparm MOL MOL.top MOL.crd
>
>
> 2) You use GAFF FF atom types: you need to use low case FF atom types.
>
> Finally, a mol2 file can be used as a prep file: You should not need to
> create prep file.
>
> I hope this helps.
>
> regards, Francois
>
>
>
> I am trying to get a prep field for an organic molecular C16H15N7O2,.
>> with RED-III according to its tutorial. How every after parmchk, the frcmod
>> give too many undefined parameter.
>> So, can the prep and frcmod field be used, if not how can I solve this
>> problem.
>>
>> Thank you for your kind help
>>
>> Pang xueqin
>>
>> Dalian ICP ACS CHINA
>>
>> Following are the frcmod for this molecular:
>> remark goes here
>> MASS
>> CA 12.010 0.360 same as c2
>> HA 1.008 0.135 same as hc
>> OH 16.000 0.465 same as oh
>> HO 1.008 0.135 same as ho
>> CT 12.010 0.878 same as c3
>> HC 1.008 0.135 same as hc
>> H1 1.008 0.135 same as hc
>> N2 14.010 0.530 same as n3
>> H 1.008 0.161 same as hn
>> CB 12.010 0.360 same as c2
>> NA 14.010 0.530 same as na
>> CR 12.010 0.360 same as c2
>> C* 12.010 0.360 same as c2
>> H4 1.008 0.135 same as ha
>> OS 16.000 0.465 same as os
>> BOND
>> CA-HA 344.30 1.087 same as c2-hc
>> CA-CA 478.40 1.387 same as ca-ca
>> CA-OH 425.40 1.333 same as c2-oh
>> OH-HO 369.60 0.974 same as ho-oh
>> CA-CT 328.30 1.508 same as c2-c3
>> CT-HC 337.30 1.092 same as c3-hc
>> CT-CT 303.10 1.535 same as c3-c3
>> CT-H1 337.30 1.092 same as c3-hc
>> CT-N2 320.60 1.470 same as c3-n3
>> N2-H 394.10 1.018 same as hn-n3
>> N2-CA 449.00 1.364 same as ca-nh
>> N2-CB 449.00 1.364 same as cc-nh
>> N2-CR 449.00 1.364 same as cc-nh
>> N2-NA 426.70 1.420 same as n3-na
>> NA-H 406.60 1.011 same as hn-na
>> NA-CR 411.10 1.391 same as c2-na
>> CR-C* 418.30 1.429 same as cc-cc
>> C*-C* 418.30 1.429 same as cc-cc
>> C*-OS 392.60 1.357 same as c2-os
>> C*-HA 344.30 1.087 same as c2-hc
>> C*-CA 411.70 1.434 same as ca-cc
>> CA-H4 344.30 1.087 same as c2-ha
>> CA-OS 392.60 1.357 same as c2-os
>> ANGLE
>> CA-CA-HA 50.300 119.700 same as c2-c2-hc
>> CA-CA-CA 67.200 119.970 same as ca-ca-ca
>> CA-CA-CT 64.300 123.420 same as c2-c2-c3
>> CA-CA-OH 71.600 122.280 same as c2-c2-oh
>> CA-OH-HO 49.900 108.980 same as c2-oh-ho
>> CA-CT-HC 47.000 110.490 same as c2-c3-hc
>> CA-CT-CT 63.700 110.960 same as c2-c3-c3
>> CT-CT-H1 46.400 110.050 same as c3-c3-hc
>> CT-CT-N2 66.200 110.380 same as c3-c3-n3
>> HC-CT-HC 39.400 108.350 same as hc-c3-hc
>> HC-CT-CT 46.400 110.050 same as c3-c3-hc
>> CT-N2-H 47.100 109.920 same as c3-n3-hn
>> CT-N2-CA 62.820 117.790 Calculated with empirical approach
>> H1-CT-H1 39.400 108.350 same as hc-c3-hc
>> H1-CT-N2 49.400 109.800 same as hc-c3-n3
>> N2-CA-N2 71.400 120.980 same as nh-ca-nh
>> H -N2-CA 49.100 119.380 same as c2-n3-hn
>> CA-N2-CA 64.300 127.460 same as ca-nh-ca
>> CA-N2-CB 66.200 124.680 same as c2-n3-c2
>> CA-N2-NA 66.760 118.340 Calculated with empirical approach
>> H -N2-H 41.300 107.130 same as hn-n3-hn
>> N2-CB-N2 72.900 115.960 same as nh-cc-nh
>> H -N2-CB 49.100 119.380 same as c2-n3-hn
>> CB-N2-CR 66.200 124.680 same as c2-n3-c2
>> CB-N2-NA 66.760 118.340 Calculated with empirical approach
>> N2-CR-NA 73.125 113.900 Calculated with empirical approach
>> N2-CR-C* 68.600 118.980 same as cc-cc-nh
>> H -N2-CR 49.100 119.380 same as c2-n3-hn
>> N2-NA-H 36.098 120.400 Calculated with empirical approach
>> N2-NA-CR 64.600 124.800 same as c2-na-n3
>> NA-CR-C* 69.800 121.380 same as c2-c2-na
>> H -NA-CR 47.600 119.280 same as c2-na-hn
>> CR-C*-C* 67.900 110.700 same as cc-cc-cc
>> CR-C*-OS 71.200 121.430 same as c2-c2-os
>> C*-C*-HA 50.300 119.700 same as c2-c2-hc
>> C*-C*-C* 67.900 110.700 same as cc-cc-cc
>> C*-OS-CA 66.000 113.140 same as c2-os-c2
>> C*-C*-OS 71.200 121.430 same as c2-c2-os
>> C*-C*-CA 67.700 111.040 same as ca-cc-cc
>> C*-CA-H4 50.000 120.940 same as c2-c2-ha
>> C*-CA-OS 71.200 121.430 same as c2-c2-os
>> HA-C*-CA 50.300 119.700 same as c2-c2-hc
>> H4-CA-OS 52.400 112.690 same as ha-c2-os
>> DIHE
>> CA-CA-CA-OH 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> CA-CA-CA-CA 1 3.625 180.000 2.000 same as X
>> -ca-ca-X
>> CA-CA-CA-HA 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> CA-CA-CT-HC 1 0.380 180.000 -3.000 same as
>> hc-c3-c2-c2
>> CA-CA-CT-HC 1 1.150 0.000 1.000 same as
>> hc-c3-c2-c2
>> CA-CA-CT-CT 1 0.000 0.000 2.000 same as X
>> -c2-c3-X
>> HA-CA-CA-HA 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> HA-CA-CA-CT 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> CA-CA-CA-CT 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> CA-CA-OH-HO 1 1.050 180.000 2.000 same as X
>> -c2-oh-X
>> HA-CA-CA-OH 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> CA-CT-CT-H1 1 0.156 0.000 3.000 same as X
>> -c3-c3-X
>> CA-CT-CT-N2 1 0.156 0.000 3.000 same as X
>> -c3-c3-X
>> CT-CT-N2-H 1 0.300 0.000 3.000 same as X
>> -c3-n3-X
>> CT-CT-N2-CA 1 0.300 0.000 3.000 same as X
>> -c3-n3-X
>> HC-CT-CT-H1 1 0.150 0.000 3.000 same as
>> hc-c3-c3-hc
>> HC-CT-CT-N2 1 0.156 0.000 3.000 same as X
>> -c3-c3-X
>> CT-N2-CA-N2 1 0.300 180.000 2.000 same as X
>> -c2-n3-X
>> H1-CT-N2-H 1 0.300 0.000 3.000 same as X
>> -c3-n3-X
>> H1-CT-N2-CA 1 0.300 0.000 3.000 same as X
>> -c3-n3-X
>> N2-CA-N2-H 1 0.300 180.000 2.000 same as X
>> -c2-n3-X
>> N2-CA-N2-CA 1 1.050 180.000 2.000 same as X
>> -ca-nh-X
>> N2-CA-N2-CB 1 1.050 180.000 2.000 same as X
>> -ca-nh-X
>> CA-N2-CB-N2 1 1.050 180.000 2.000 same as X
>> -cc-nh-X
>> N2-CA-N2-NA 1 0.300 180.000 2.000 same as X
>> -c2-n3-X
>> CA-N2-NA-H 1 1.600 0.000 2.000 same as X
>> -n3-na-X
>> CA-N2-NA-CR 1 1.600 0.000 2.000 same as X
>> -n3-na-X
>> N2-CB-N2-H 1 0.300 180.000 2.000 same as X
>> -c2-n3-X
>> N2-CB-N2-CR 1 1.050 180.000 2.000 same as X
>> -cc-nh-X
>> N2-CB-N2-NA 1 0.300 180.000 2.000 same as X
>> -c2-n3-X
>> CB-N2-CR-NA 1 0.300 180.000 2.000 same as X
>> -c2-n3-X
>> CB-N2-CR-C* 1 1.050 180.000 2.000 same as X
>> -cc-nh-X
>> CB-N2-NA-H 1 1.600 0.000 2.000 same as X
>> -n3-na-X
>> CB-N2-NA-CR 1 1.600 0.000 2.000 same as X
>> -n3-na-X
>> N2-CR-NA-N2 1 0.625 180.000 2.000 same as X
>> -c2-na-X
>> N2-CR-NA-H 1 0.625 180.000 2.000 same as X
>> -c2-na-X
>> N2-CR-C*-C* 1 4.000 180.000 2.000 same as X
>> -cc-cc-X
>> N2-CR-C*-OS 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> H -N2-CR-NA 1 0.300 180.000 2.000 same as X
>> -c2-n3-X
>> H -N2-CR-C* 1 0.300 180.000 2.000 same as X
>> -c2-n3-X
>> N2-NA-CR-C* 1 0.625 180.000 2.000 same as X
>> -c2-na-X
>> NA-CR-C*-C* 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> NA-CR-C*-OS 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> H -NA-CR-C* 1 0.625 180.000 2.000 same as X
>> -c2-na-X
>> CR-C*-C*-HA 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> CR-C*-C*-C* 1 4.000 180.000 2.000 same as X
>> -cc-cc-X
>> CR-C*-OS-CA 1 1.050 180.000 2.000 same as X
>> -c2-os-X
>> C*-C*-C*-HA 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> C*-C*-C*-CA 1 4.000 180.000 2.000 same as X
>> -cc-cc-X
>> C*-OS-CA-C* 1 1.050 180.000 2.000 same as X
>> -c2-os-X
>> C*-OS-CA-H4 1 1.050 180.000 2.000 same as X
>> -c2-os-X
>> C*-C*-OS-CA 1 1.050 180.000 2.000 same as X
>> -c2-os-X
>> C*-C*-CA-H4 1 4.000 180.000 2.000 same as X
>> -cc-cc-X
>> C*-C*-CA-OS 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> HA-C*-C*-OS 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> HA-C*-C*-HA 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> HA-C*-C*-CA 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> C*-C*-C*-OS 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> HA-C*-CA-H4 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> HA-C*-CA-OS 1 6.650 180.000 2.000 same as X
>> -c2-c2-X
>> IMPROPER
>> CA-CA-CA-HA 1.1 180.0 2.0 Using default
>> value
>> CA-CA-CA-OH 1.1 180.0 2.0 Using default
>> value
>> CA-CA-CA-CT 1.1 180.0 2.0 Using default
>> value
>> CA-CT-N2-H 1.1 180.0 2.0 Using default
>> value
>> N2-N2-CA-N2 1.1 180.0 2.0 Using default
>> value
>> CA-CA-N2-H 1.1 180.0 2.0 Using default
>> value
>> CA-H -N2-H 1.1 180.0 2.0 Using default
>> value
>> CA-CB-N2-H 1.1 180.0 2.0 Using default
>> value
>> N2-N2-CB-N2 1.1 180.0 2.0 Using default
>> value
>> CB-CR-N2-H 1.1 180.0 2.0 Using default
>> value
>> CA-CB-N2-NA 1.1 180.0 2.0 Using default
>> value
>> CR-H -NA-N2 1.1 180.0 2.0 Using default
>> value
>> C*-N2-CR-NA 1.1 180.0 2.0 Using default
>> value
>> C*-CR-C*-OS 1.1 180.0 2.0 Using default
>> value
>> C*-C*-C*-HA 1.1 180.0 2.0 Using default
>> value
>> C*-CA-C*-HA 1.1 180.0 2.0 Using default
>> value
>> C*-H4-CA-OS 1.1 180.0 2.0 Using default
>> value
>> NONBON
>> CA 1.9080 0.0860 same as ca
>> HA 1.4870 0.0157 same as hc
>> OH 1.7210 0.2104 same as oh
>> HO 0.0000 0.0000 same as ho
>> CT 1.9080 0.1094 same as c3
>> HC 1.4870 0.0157 same as hc
>> H1 1.4870 0.0157 same as hc
>> N2 1.8240 0.1700 same as nh
>> H 0.6000 0.0157 same as hn
>> CB 1.9080 0.0860 same as cc
>> NA 1.8240 0.1700 same as na
>> CR 1.9080 0.0860 same as cc
>> C* 1.9080 0.0860 same as cc
>> H4 1.4870 0.0157 same as hc
>> OS 1.6837 0.1700 same as os
>>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber