This tutorial is seriously old, need to be updated. I also did these resp fits ages ago, hopefully my notes make sense to both of us, apologies if not.
The espgen and respgen program info are here: http://ambermd.org/antechamber/ac.html
1. Did you try espgen on the Gaussian output log file ?
i.e.
espgen -i gaussian.log -o gaussian.esp
2. For the resp command, you need to prepare a resp.in file first. You can use respgen to make sure the resp.in file is the right format and then edit by hand.
In the resp.in file, In line 9, state total charge and number of atoms. Following, 1st column represents atomic numbers and 2nd column contains what you want to do for each atom partial charge. For 2nd column, -1 means refer to a reference charge represented in the resp.qin file, 0 means let charge float ; n means link charge change with residue n.
3. To call the resp command next with this resp.in file,
resp -O -i resp.in -t resp.chg -q resp.qin -e gaussian.esp -o resp.out
Example of a resp.in file:
ln5 RESP run #1
&cntrl
ihfree=1,
qwt=0.0005,
iqopt=2
/
1.0
Mol1
-1 105
1 -1
6 -1
1 -1
1 -1
6 -1
8 0
7 0
1 -1
6 -1
1 3
…….. (file continues)
Prem
> On Jul 1, 2019, at 3:38 PM, David Cerutti <dscerutti.gmail.com> wrote:
>
> Not sure--I try to insulate myself from Gaussian but their listserv is
> active and they'll probably be able to advise you. If you can get the
> cubegen file one way or another, the electrostatic potential fitting is
> easy to do.
>
> Dave
>
>
> On Mon, Jul 1, 2019 at 3:35 PM Sadaf Rani <sadafrani6.gmail.com> wrote:
>
>> Dear Amber and Dave
>> I did optimisation in gaussian in solvent for ligand and calculated ESP as
>> mentioned:
>> https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial1%2Fsection1.htm&data=02%7C01%7Cps958%40iqb.rutgers.edu%7C9fabe3c5fe9747b4677608d6fe5bbb76%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636976067276551184&sdata=E06Hg8Gsq7Y%2B13Sm6JjkPWx5vQpdz3UxQadPbt98EHE%3D&reserved=0
>> now I use
>> resp -O -i resp.in -o resp.out -p punch -q qin -t qout
>>
>> it dont work it gives following error:-
>> Unit 10 Error on OPEN: espot
>>
>> what wrong I am putting here?
>>
>> Please suggest
>> thank you
>>
>> Sadaf
>>
>> On Mon, Jul 1, 2019 at 5:57 PM David Cerutti <dscerutti.gmail.com> wrote:
>>
>>> The sustiva tutorial is the place to start if you want to create an Amber
>>> library file for your residue. Once you've got that, if the vagaries of
>>> Antechamber's RESP are not to your liking, you can look through the mdgx
>>> charge fitting tutorials:
>>>
>>> https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial28%2Findex.php&data=02%7C01%7Cps958%40iqb.rutgers.edu%7C9fabe3c5fe9747b4677608d6fe5bbb76%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636976067276551184&sdata=WM5zaN6l7vivMU5gXx41UA3Bj0hIE4zK%2FRzmx0P%2F94k%3D&reserved=0
>>>
>>> The IPolQ charge generation scheme is very involved and still laborious,
>>> but a lot of this owes to what I think of as a converged solution to the
>>> charge set (needs dozens of conformations, plus iterations on top of
>>> that). If all you want is to get a solution to the monopole distribution
>>> that optimizes the electrostatics according to a target QM method like
>> HF /
>>> 6-31G*, this would be really easy to do with mdgx once you have the
>> library
>>> files and prmtops.
>>>
>>> If you like one conformation in particular, you can use Gaussian to run
>> the
>>> QM and generate cubegen-format files that mdgx will read to give you the
>>> electrostatics, or I could even show you how to bypass most of the IPolQ
>>> procedure and use ORCA to generate the cubegen-format file. Bottom line,
>>> if you want something a little more hands-on, and you have Gaussian or
>> ORCA
>>> available, mdgx can give you fitted charges and an analysis of the
>>> electrostatics versus QM. You can play with things like the extent of
>>> space around the molecule to use in fitting charges, and see how the
>>> results change if you include new conformations.
>>>
>>> Dave
>>>
>>>
>>> On Mon, Jul 1, 2019 at 12:37 PM Sadaf Rani <sadafrani6.gmail.com> wrote:
>>>
>>>> thank you Martis
>>>> I have tried it earlier but during the course of this process one of
>>> proton
>>>> shifts to another atom when I observe sqm.pdb. As antechamber uses gas
>>>> phase calculation method.
>>>> That is why I am calculating charges by RESP method.
>>>> Any further suggestion please let me know.
>>>> thank you
>>>>
>>>> Sadaf
>>>>
>>>>
>>>> On Mon, Jul 1, 2019 at 4:25 PM Elvis Martis <elvis_bcp.elvismartis.in>
>>>> wrote:
>>>>
>>>>> Hello
>>>>> You are looking at an advanced tutorial.
>>>>> Please have a look at this one
>>>>> https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fbasic%2Ftutorial4b%2Findex.html&data=02%7C01%7Cps958%40iqb.rutgers.edu%7C9fabe3c5fe9747b4677608d6fe5bbb76%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636976067276551184&sdata=XFj6h%2FNrd0u9NI1mLu4QfSVC36uhal9g8WuZuFrivB4%3D&reserved=0
>>>>> I guess this is best suited for you.
>>>>>
>>>>> On Monday, July 1, 2019, Sadaf Rani <sadafrani6.gmail.com> wrote:
>>>>>
>>>>>> thank you Martis
>>>>>> but what about RESP fitting as mentioend in this tutorial:
>>>>>> https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial1%2Fsection1.htm&data=02%7C01%7Cps958%40iqb.rutgers.edu%7C9fabe3c5fe9747b4677608d6fe5bbb76%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636976067276551184&sdata=E06Hg8Gsq7Y%2B13Sm6JjkPWx5vQpdz3UxQadPbt98EHE%3D&reserved=0
>>>>>>
>>>>>>
>>>>>> Looking forward to hear from you soon
>>>>>>
>>>>>> thank you
>>>>>>
>>>>>> Sadaf
>>>>>>
>>>>>> On Mon, Jul 1, 2019 at 12:21 PM Elvis Martis <
>>> elvis.martis.bcp.edu.in>
>>>>>> wrote:
>>>>>>
>>>>>>> Next you must do this
>>>>>>> parmchk2 -i bg6.in -f prepi -o bg6.frcmod
>>>>>>>
>>>>>>>
>>>>>>> Best Regards
>>>>>>>
>>>>>>> Elvis Martis
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ________________________________
>>>>>>> From: Sadaf Rani <sadafrani6.gmail.com>
>>>>>>> Sent: 01 July 2019 16:09
>>>>>>> To: AMBER Mailing List
>>>>>>> Subject: [AMBER] RESP charge calculation
>>>>>>>
>>>>>>> Dear Amber users
>>>>>>> I am trying to calculate RESP charges for my ligand by method as
>>>>>> mentioned
>>>>>>> in following link:-
>>>>>>> https://nam02.safelinks.protection.outlook.com/?url=http:%2F%2Fsigne.teokem.lu.se%2F~ulf%2FMethods%2Fresp.html&data=02%7C01%7Cps958%40iqb.rutgers.edu%7C9fabe3c5fe9747b4677608d6fe5bbb76%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636976067276551184&sdata=jGL%2Bd7jPvux8mZyZSN%2Fh7yKpzAayvK%2FBSINGgYSpeeY%3D&reserved=0
>>>>>>>
>>>>>>> when I am using this command
>>>>>>> antechamber -fi gout -fo prepi -c resp -i BG6.out -o bg6.in -rn
>>> BG6
>>>>>> -pf y
>>>>>>> (BG6 is the ligand here)
>>>>>>> I get following files:
>>>>>>> bg6.in, esout, qout and QOUT
>>>>>>> what to do further is not very clear
>>>>>>> Can any body suggest me?
>>>>>>> thank you
>>>>>>> Sadaf
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7Cps958%40iqb.rutgers.edu%7C9fabe3c5fe9747b4677608d6fe5bbb76%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636976067276561180&sdata=1Tgzr6jEQMI96QRX2QzLfHNqvV2h15xR8pSN%2FjpSsRA%3D&reserved=0
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7Cps958%40iqb.rutgers.edu%7C9fabe3c5fe9747b4677608d6fe5bbb76%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636976067276561180&sdata=1Tgzr6jEQMI96QRX2QzLfHNqvV2h15xR8pSN%2FjpSsRA%3D&reserved=0
>>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7Cps958%40iqb.rutgers.edu%7C9fabe3c5fe9747b4677608d6fe5bbb76%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636976067276561180&sdata=1Tgzr6jEQMI96QRX2QzLfHNqvV2h15xR8pSN%2FjpSsRA%3D&reserved=0
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Best Regards
>>>>> Elvis Martis
>>>>> Mumbai.
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7Cps958%40iqb.rutgers.edu%7C9fabe3c5fe9747b4677608d6fe5bbb76%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636976067276561180&sdata=1Tgzr6jEQMI96QRX2QzLfHNqvV2h15xR8pSN%2FjpSsRA%3D&reserved=0
>>>>>
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>>>>
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Received on Mon Jul 01 2019 - 18:00:02 PDT
